HEADER OXIDOREDUCTASE 29-APR-15 5A1F
TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PLU1 IN COMPLEX WITH N-
TITLE 2 OXALYLGLYCINE.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE
COMPND 3 5B;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: JMJC DOMAIN, RESIDUES, JMJC DOMAIN, RESIDUES;
COMPND 6 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B,
COMPND 7 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA-
COMPND 8 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1, CANCER/TESTIS ANTIGEN 31, CT31,
COMPND 9 HISTONE DEMETHYLASE JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN
COMPND 10 1B, PLU-1, RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1;
COMPND 11 EC: 1.14.11.-, 1.14.11.-;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: KDM5B, JARID1B, PLU1, RBBP2H1;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE
KEYWDS OXIDOREDUCTASE, LYSINE-SPECIFIC DEMETHYLASE 5B
EXPDTA X-RAY DIFFRACTION
AUTHOR V.SRIKANNATHASAN,C.JOHANSSON,C.STRAIN-DAMERELL,C.GILEADI,A.SZYKOWSKA,
AUTHOR 2 K.KUPINSKA,J.KOPEC,T.KROJER,H.STEUBER,F.VON DELFT,N.A.BURGESS-BROWN,
AUTHOR 3 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN
REVDAT 7 10-JAN-24 5A1F 1 REMARK LINK
REVDAT 6 29-JUN-16 5A1F 1 JRNL
REVDAT 5 01-JUN-16 5A1F 1 JRNL
REVDAT 4 25-MAY-16 5A1F 1 JRNL
REVDAT 3 20-MAY-15 5A1F 1 SOURCE REMARK
REVDAT 2 13-MAY-15 5A1F 1 TITLE AUTHOR
REVDAT 1 06-MAY-15 5A1F 0
JRNL AUTH C.JOHANSSON,S.VELUPILLAI,A.TUMBER,A.SZYKOWSKA,E.S.HOOKWAY,
JRNL AUTH 2 R.P.NOWAK,C.STRAIN-DAMERELL,C.GILEADI,M.PHILPOTT,
JRNL AUTH 3 N.BURGESS-BROWN,N.WU,J.KOPEC,A.NUZZI,H.STEUBER,U.EGNER,
JRNL AUTH 4 V.BADOCK,S.MUNRO,N.B.LATHANGUE,S.WESTAWAY,J.BROWN,
JRNL AUTH 5 N.ATHANASOU,R.PRINJHA,P.E.BRENNAN,U.OPPERMANN
JRNL TITL STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE
JRNL TITL 2 DEMETHYLASE INHIBITOR DEVELOPMENT.
JRNL REF NAT.CHEM.BIOL. V. 12 539 2016
JRNL REFN ISSN 1552-4450
JRNL PMID 27214403
JRNL DOI 10.1038/NCHEMBIO.2087
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0107
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 50341
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.201
REMARK 3 R VALUE (WORKING SET) : 0.199
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2629
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3678
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.3020
REMARK 3 BIN FREE R VALUE SET COUNT : 174
REMARK 3 BIN FREE R VALUE : 0.3250
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3603
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 62
REMARK 3 SOLVENT ATOMS : 204
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.60
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.41000
REMARK 3 B22 (A**2) : 0.41000
REMARK 3 B33 (A**2) : -1.32000
REMARK 3 B12 (A**2) : 0.20000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.143
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.166
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3797 ; 0.011 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3488 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5155 ; 1.503 ; 1.960
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8048 ; 0.985 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 6.391 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;35.102 ;23.523
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 608 ;15.113 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.544 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.088 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4224 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 881 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1808 ; 3.070 ; 4.569
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1807 ; 3.064 ; 4.567
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2258 ; 4.623 ; 6.833
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1988 ; 3.638 ; 4.945
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY SOME SIDE CHAINS
REMARK 3 REMOVED AND SOME OF THE RESIDUES HAVE ALTERNATIVE CONFIRMATION.
REMARK 4
REMARK 4 5A1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-15.
REMARK 100 THE DEPOSITION ID IS D_1290063710.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-MAR-15
REMARK 200 TEMPERATURE (KELVIN) : 287
REMARK 200 PH : 8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.91742
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52970
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 19.770
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 11.50
REMARK 200 R MERGE (I) : 0.09000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 11.50
REMARK 200 R MERGE FOR SHELL (I) : 0.09000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.420
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CCP4I
REMARK 200 STARTING MODEL: PDB ENTRY 4GIO
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 70.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 0.8M POTASSIUM
REMARK 280 PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.41933
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.70967
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.06450
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.35483
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 126.77417
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.41933
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 50.70967
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.35483
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 76.06450
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 126.77417
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 LYS A 100
REMARK 465 LEU A 101
REMARK 465 ALA A 374
REMARK 465 GLY A 443
REMARK 465 LYS A 444
REMARK 465 ILE A 445
REMARK 465 LYS A 446
REMARK 465 LEU A 447
REMARK 465 SER A 754
REMARK 465 TYR A 755
REMARK 465 ASN A 756
REMARK 465 GLU A 757
REMARK 465 TRP A 758
REMARK 465 ALA A 759
REMARK 465 LEU A 760
REMARK 465 ASN A 761
REMARK 465 VAL A 762
REMARK 465 ASN A 763
REMARK 465 GLU A 764
REMARK 465 ALA A 765
REMARK 465 LEU A 766
REMARK 465 GLU A 767
REMARK 465 ALA A 768
REMARK 465 LYS A 769
REMARK 465 ILE A 770
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 40 CG CD OE1 OE2
REMARK 470 LEU A 81 CG CD1 CD2
REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2
REMARK 470 VAL A 99 CG1 CG2
REMARK 470 GLU A 404 CG CD OE1 OE2
REMARK 470 LYS A 432 CG CD CE NZ
REMARK 470 PHE A 434 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 ASP A 442 CG OD1 OD2
REMARK 470 GLU A 450 CG CD OE1 OE2
REMARK 470 GLU A 452 CG CD OE1 OE2
REMARK 470 GLN A 545 CG CD OE1 NE2
REMARK 470 LYS A 653 CE NZ
REMARK 470 LYS A 720 CG CD CE NZ
REMARK 470 LYS A 749 CE NZ
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OE1 GLU A 515 O2 EDO A 1764 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 584 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 TRP A 70 97.09 -68.02
REMARK 500 LEU A 93 -3.19 60.77
REMARK 500 PHE A 434 -72.85 -83.70
REMARK 500 PHE A 493 -9.20 77.55
REMARK 500 ALA A 538 68.63 -152.68
REMARK 500 HIS A 550 32.55 -141.46
REMARK 500 PHE A 700 -54.96 -149.09
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1757 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 91 OD1
REMARK 620 2 THR A 416 O 114.7
REMARK 620 3 GLU A 419 O 104.2 66.3
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A1758 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 499 NE2
REMARK 620 2 GLU A 501 OE2 100.0
REMARK 620 3 HIS A 587 NE2 88.4 82.1
REMARK 620 4 OGA A1756 O2' 88.5 170.9 101.5
REMARK 620 5 OGA A1756 O1 167.7 92.2 93.1 79.3
REMARK 620 6 HOH A2098 O 88.7 93.0 173.7 84.0 91.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1754 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 692 SG
REMARK 620 2 CYS A 695 SG 106.9
REMARK 620 3 CYS A 715 SG 117.1 112.5
REMARK 620 4 HIS A 718 ND1 113.4 109.0 97.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1755 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 706 SG
REMARK 620 2 CYS A 708 SG 115.6
REMARK 620 3 CYS A 723 SG 111.5 107.2
REMARK 620 4 CYS A 725 SG 103.3 111.8 107.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1754
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1755
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 1756
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1757
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1758
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1759
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1760
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1761
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1762
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1763
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1764
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1765
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1766
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1767
DBREF 5A1F A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101
DBREF 5A1F A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770
SEQADV 5A1F SER A -1 UNP Q9UGL1 EXPRESSION TAG
SEQADV 5A1F MET A 0 UNP Q9UGL1 EXPRESSION TAG
SEQRES 1 A 475 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU
SEQRES 2 A 475 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE
SEQRES 3 A 475 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS
SEQRES 4 A 475 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA
SEQRES 5 A 475 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN
SEQRES 6 A 475 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU
SEQRES 7 A 475 ALA ARG ASP TYR THR LEU ARG THR PHE GLY GLU MET ALA
SEQRES 8 A 475 ASP ALA PHE LYS SER ASP TYR PHE ASN MET PRO VAL HIS
SEQRES 9 A 475 MET VAL PRO THR GLU LEU VAL GLU LYS GLU PHE TRP ARG
SEQRES 10 A 475 LEU VAL SER THR ILE GLU GLU ASP VAL THR VAL GLU TYR
SEQRES 11 A 475 GLY ALA ASP ILE ALA SER LYS GLU PHE GLY SER GLY PHE
SEQRES 12 A 475 PRO VAL ARG ASP GLY LYS ILE LYS LEU SER PRO GLU GLU
SEQRES 13 A 475 GLU GLU TYR LEU ASP SER GLY TRP ASN LEU ASN ASN MET
SEQRES 14 A 475 PRO VAL MET GLU GLN SER VAL LEU ALA HIS ILE THR ALA
SEQRES 15 A 475 ASP ILE CYS GLY MET LYS LEU PRO TRP LEU TYR VAL GLY
SEQRES 16 A 475 MET CYS PHE SER SER PHE CYS TRP HIS ILE GLU ASP HIS
SEQRES 17 A 475 TRP SER TYR SER ILE ASN TYR LEU HIS TRP GLY GLU PRO
SEQRES 18 A 475 LYS THR TRP TYR GLY VAL PRO GLY TYR ALA ALA GLU GLN
SEQRES 19 A 475 LEU GLU ASN VAL MET LYS LYS LEU ALA PRO GLU LEU PHE
SEQRES 20 A 475 VAL SER GLN PRO ASP LEU LEU HIS GLN LEU VAL THR ILE
SEQRES 21 A 475 MET ASN PRO ASN THR LEU MET THR HIS GLU VAL PRO VAL
SEQRES 22 A 475 TYR ARG THR ASN GLN CYS ALA GLY GLU PHE VAL ILE THR
SEQRES 23 A 475 PHE PRO ARG ALA TYR HIS SER GLY PHE ASN GLN GLY PHE
SEQRES 24 A 475 ASN PHE ALA GLU ALA VAL ASN PHE CYS THR VAL ASP TRP
SEQRES 25 A 475 LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS TYR ARG LEU
SEQRES 26 A 475 LEU HIS ARG TYR CYS VAL PHE SER HIS ASP GLU MET ILE
SEQRES 27 A 475 CYS LYS MET ALA SER LYS ALA ASP VAL LEU ASP VAL VAL
SEQRES 28 A 475 VAL ALA SER THR VAL GLN LYS ASP MET ALA ILE MET ILE
SEQRES 29 A 475 GLU ASP GLU LYS ALA LEU ARG GLU THR VAL ARG LYS LEU
SEQRES 30 A 475 GLY VAL ILE ASP SER GLU ARG MET ASP PHE GLU LEU LEU
SEQRES 31 A 475 PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS LYS THR THR
SEQRES 32 A 475 CYS PHE MET SER ALA ILE SER CYS SER CYS LYS PRO GLY
SEQRES 33 A 475 LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU LEU CYS SER
SEQRES 34 A 475 CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR ARG TYR THR
SEQRES 35 A 475 LEU ASP ASP LEU TYR PRO MET MET ASN ALA LEU LYS LEU
SEQRES 36 A 475 ARG ALA GLU SER TYR ASN GLU TRP ALA LEU ASN VAL ASN
SEQRES 37 A 475 GLU ALA LEU GLU ALA LYS ILE
HET ZN A1754 1
HET ZN A1755 1
HET OGA A1756 10
HET MN A1757 1
HET MN A1758 1
HET PO4 A1759 5
HET EPE A1760 15
HET EDO A1761 4
HET EDO A1762 4
HET EDO A1763 4
HET EDO A1764 4
HET EDO A1765 4
HET EDO A1766 4
HET EDO A1767 4
HETNAM ZN ZINC ION
HETNAM OGA N-OXALYLGLYCINE
HETNAM MN MANGANESE (II) ION
HETNAM PO4 PHOSPHATE ION
HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EPE HEPES
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN 2(ZN 2+)
FORMUL 4 OGA C4 H5 N O5
FORMUL 5 MN 2(MN 2+)
FORMUL 7 PO4 O4 P 3-
FORMUL 8 EPE C8 H18 N2 O4 S
FORMUL 9 EDO 7(C2 H6 O2)
FORMUL 16 HOH *204(H2 O)
HELIX 1 1 SER A 38 ALA A 43 1 6
HELIX 2 2 ASP A 44 GLU A 57 1 14
HELIX 3 3 LEU A 379 ASN A 395 1 17
HELIX 4 4 PRO A 397 VAL A 401 5 5
HELIX 5 5 PRO A 402 THR A 416 1 15
HELIX 6 6 SER A 448 SER A 457 1 10
HELIX 7 7 ASN A 462 MET A 467 1 6
HELIX 8 8 SER A 470 ILE A 475 5 6
HELIX 9 9 ILE A 479 LEU A 484 1 6
HELIX 10 10 GLU A 501 SER A 505 5 5
HELIX 11 11 PRO A 523 TYR A 525 5 3
HELIX 12 12 ALA A 526 ALA A 538 1 13
HELIX 13 13 PRO A 539 VAL A 543 5 5
HELIX 14 14 ASP A 547 HIS A 550 5 4
HELIX 15 15 ASN A 557 HIS A 564 1 8
HELIX 16 16 TRP A 607 HIS A 622 1 16
HELIX 17 17 SER A 628 SER A 638 1 11
HELIX 18 18 LYS A 639 LEU A 643 5 5
HELIX 19 19 ASP A 644 LEU A 672 1 29
HELIX 20 20 ASP A 681 LEU A 685 5 5
HELIX 21 21 PRO A 686 ARG A 690 5 5
HELIX 22 22 HIS A 718 LEU A 722 5 5
HELIX 23 23 PRO A 726 TYR A 728 5 3
HELIX 24 24 THR A 737 GLU A 753 1 17
SHEET 1 AA 8 VAL A 34 PHE A 35 0
SHEET 2 AA 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35
SHEET 3 AA 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64
SHEET 4 AA 8 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581
SHEET 5 AA 8 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512
SHEET 6 AA 8 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599
SHEET 7 AA 8 THR A 422 ILE A 429 -1 O GLY A 426 N VAL A 489
SHEET 8 AA 8 ARG A 86 ARG A 89 -1 O ARG A 86 N TYR A 425
SHEET 1 AB 2 HIS A 82 PHE A 83 0
SHEET 2 AB 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83
SHEET 1 AC 2 GLN A 96 THR A 97 0
SHEET 2 AC 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96
SHEET 1 AD 4 SER A 495 HIS A 499 0
SHEET 2 AD 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499
SHEET 3 AD 4 LYS A 517 GLY A 521 -1 O THR A 518 N PHE A 590
SHEET 4 AD 4 TYR A 569 GLN A 573 -1 O TYR A 569 N GLY A 521
SHEET 1 AE 3 ASP A 676 ARG A 679 0
SHEET 2 AE 3 TYR A 730 TYR A 734 1 O TYR A 730 N ASP A 676
SHEET 3 AE 3 SER A 702 CYS A 706 -1 O ALA A 703 N ARG A 733
LINK OD1 ASN A 91 MN MN A1757 1555 1555 2.62
LINK O THR A 416 MN MN A1757 1555 1555 2.76
LINK O GLU A 419 MN MN A1757 1555 1555 2.76
LINK NE2 HIS A 499 MN MN A1758 1555 1555 2.22
LINK OE2 GLU A 501 MN MN A1758 1555 1555 2.06
LINK NE2 HIS A 587 MN MN A1758 1555 1555 2.17
LINK SG CYS A 692 ZN ZN A1754 1555 1555 2.22
LINK SG CYS A 695 ZN ZN A1754 1555 1555 2.41
LINK SG CYS A 706 ZN ZN A1755 1555 1555 2.31
LINK SG CYS A 708 ZN ZN A1755 1555 1555 2.27
LINK SG CYS A 715 ZN ZN A1754 1555 1555 2.23
LINK ND1 HIS A 718 ZN ZN A1754 1555 1555 2.19
LINK SG CYS A 723 ZN ZN A1755 1555 1555 2.36
LINK SG CYS A 725 ZN ZN A1755 1555 1555 2.53
LINK O2' OGA A1756 MN MN A1758 1555 1555 2.06
LINK O1 OGA A1756 MN MN A1758 1555 1555 2.20
LINK MN MN A1758 O HOH A2098 1555 1555 1.90
SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718
SITE 1 AC2 4 CYS A 706 CYS A 708 CYS A 723 CYS A 725
SITE 1 AC3 14 PHE A 496 HIS A 499 GLU A 501 SER A 507
SITE 2 AC3 14 ASN A 509 LYS A 517 TRP A 519 HIS A 587
SITE 3 AC3 14 ALA A 599 MN A1758 EDO A1765 EDO A1766
SITE 4 AC3 14 HOH A2098 HOH A2203
SITE 1 AC4 5 LEU A 90 ASN A 91 LEU A 413 THR A 416
SITE 2 AC4 5 GLU A 419
SITE 1 AC5 5 HIS A 499 GLU A 501 HIS A 587 OGA A1756
SITE 2 AC5 5 HOH A2098
SITE 1 AC6 4 HIS A 622 LYS A 694 HIS A 718 HOH A2143
SITE 1 AC7 16 ILE A 500 TRP A 504 GLU A 531 MET A 534
SITE 2 AC7 16 LEU A 541 LEU A 552 VAL A 553 ARG A 584
SITE 3 AC7 16 TYR A 586 HIS A 617 TYR A 618 LEU A 621
SITE 4 AC7 16 ARG A 623 HOH A2096 HOH A2101 HOH A2149
SITE 1 AC8 7 ILE A 475 ALA A 477 PHE A 627 SER A 628
SITE 2 AC8 7 GLU A 631 MET A 632 HOH A2184
SITE 1 AC9 9 ASP A 688 GLU A 689 ARG A 690 GLN A 691
SITE 2 AC9 9 VAL A 693 GLY A 711 LEU A 712 LEU A 713
SITE 3 AC9 9 HOH A2204
SITE 1 BC1 4 VAL A 674 ILE A 675 HOH A2167 HOH A2171
SITE 1 BC2 8 ALA A 386 ASP A 387 LYS A 390 MET A 491
SITE 2 BC2 8 CYS A 492 GLU A 515 GLY A 593 PHE A 594
SITE 1 BC3 7 TYR A 425 SER A 494 SER A 495 LYS A 517
SITE 2 BC3 7 ASN A 591 OGA A1756 HOH A2203
SITE 1 BC4 6 TYR A 488 GLU A 501 ASN A 601 OGA A1756
SITE 2 BC4 6 HOH A2090 HOH A2098
SITE 1 BC5 6 ASP A 630 CYS A 699 PHE A 700 MET A 701
SITE 2 BC5 6 SER A 702 HOH A2154
CRYST1 141.855 141.855 152.129 90.00 90.00 120.00 P 65 2 2 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.007049 0.004070 0.000000 0.00000
SCALE2 0.000000 0.008140 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006573 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
