HEADER OXIDOREDUCTASE 31-MAY-10 3N9O
TITLE CEKDM7A FROM C.ELEGANS, COMPLEX WITH H3K4ME3 PEPTIDE, H3K9ME2 PEPTIDE
TITLE 2 AND NOG
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PHD DOMAIN, UNP RESIDUES 201-724;
COMPND 5 SYNONYM: LYSINE DEMETHYLASE;
COMPND 6 EC: 1.14.11.27;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: HISTONE H3 PEPTIDE;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: JMJC DOMAIN, UNP RESIDUES 2-16;
COMPND 12 ENGINEERED: YES;
COMPND 13 OTHER_DETAILS: H3K4ME3;
COMPND 14 MOL_ID: 3;
COMPND 15 MOLECULE: HISTONE H3 PEPTIDE;
COMPND 16 CHAIN: C;
COMPND 17 FRAGMENT: JMJC DOMAIN, UNP RESIDUES 2-18;
COMPND 18 ENGINEERED: YES;
COMPND 19 OTHER_DETAILS: H3K9ME2
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS;
SOURCE 3 ORGANISM_TAXID: 6239;
SOURCE 4 GENE: F29B9.2;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B;
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS;
SOURCE 13 ORGANISM_TAXID: 6239;
SOURCE 14 OTHER_DETAILS: CHEMICAL SYNTHESIS, PURCHASED FROM A COMPANY;
SOURCE 15 MOL_ID: 3;
SOURCE 16 SYNTHETIC: YES;
SOURCE 17 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS;
SOURCE 18 ORGANISM_TAXID: 6239;
SOURCE 19 OTHER_DETAILS: CHEMICAL SYNTHESIS, PURCHASED FROM A COMPANY
KEYWDS HISTONE, METHYLATION, DEMETHYLASE, PHD, JMJC, FE(II) AND ALPHA-KG
KEYWDS 2 (ALPHA-KETOGLUTARATE)-DEPENDENT DIOXYGENASE FAMILY, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.YANG,L.HU,P.WANG,H.HOU,C.D.CHEN,Y.XU
REVDAT 3 01-NOV-23 3N9O 1 REMARK SEQADV LINK
REVDAT 2 11-AUG-10 3N9O 1 JRNL
REVDAT 1 30-JUN-10 3N9O 0
JRNL AUTH Y.YANG,L.HU,P.WANG,H.HOU,Y.LIN,Y.LIU,Z.LI,R.GONG,X.FENG,
JRNL AUTH 2 L.ZHOU,W.ZHANG,Y.DONG,H.YANG,H.LIN,Y.WANG,C.D.CHEN,Y.XU
JRNL TITL STRUCTURAL INSIGHTS INTO A DUAL-SPECIFICITY HISTONE
JRNL TITL 2 DEMETHYLASE CEKDM7A FROM CAENORHABDITIS ELEGANS
JRNL REF CELL RES. V. 20 886 2010
JRNL REFN ISSN 1001-0602
JRNL PMID 20567261
JRNL DOI 10.1038/CR.2010.86
REMARK 2
REMARK 2 RESOLUTION. 2.31 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.28
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 27443
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.201
REMARK 3 R VALUE (WORKING SET) : 0.199
REMARK 3 FREE R VALUE : 0.242
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040
REMARK 3 FREE R VALUE TEST SET COUNT : 1383
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 44.2880 - 4.9721 1.00 2831 139 0.1917 0.2214
REMARK 3 2 4.9721 - 3.9473 1.00 2699 147 0.1565 0.1949
REMARK 3 3 3.9473 - 3.4485 1.00 2647 150 0.1864 0.2489
REMARK 3 4 3.4485 - 3.1333 1.00 2636 155 0.2046 0.2350
REMARK 3 5 3.1333 - 2.9088 1.00 2669 129 0.2221 0.2925
REMARK 3 6 2.9088 - 2.7373 1.00 2629 138 0.2162 0.2776
REMARK 3 7 2.7373 - 2.6002 1.00 2620 134 0.2199 0.2375
REMARK 3 8 2.6002 - 2.4871 1.00 2609 140 0.2226 0.2440
REMARK 3 9 2.4871 - 2.3913 0.97 2524 133 0.2307 0.2920
REMARK 3 10 2.3913 - 2.3088 0.84 2196 118 0.2619 0.3235
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.33
REMARK 3 B_SOL : 37.57
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.690
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.130
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 39.49
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.66
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.94580
REMARK 3 B22 (A**2) : 2.22680
REMARK 3 B33 (A**2) : -3.17260
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 4209
REMARK 3 ANGLE : 1.016 5680
REMARK 3 CHIRALITY : 0.073 584
REMARK 3 PLANARITY : 0.008 731
REMARK 3 DIHEDRAL : 18.202 1567
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3N9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-10.
REMARK 100 THE DEPOSITION ID IS D_1000059555.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-MAY-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL17U
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.2828
REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27497
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASES
REMARK 200 STARTING MODEL: PDB ENTRY 3N9M
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.11
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.2M SODIUM FLUORIDE,
REMARK 280 0.1M BIS-TRIS OR HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
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 -1.000000 0.000000 0.000000 34.54500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.36350
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.68950
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.36350
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.54500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.68950
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 23250 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 GLU A 184
REMARK 465 PHE A 185
REMARK 465 HIS A 186
REMARK 465 MET A 187
REMARK 465 GLU A 188
REMARK 465 GLN A 189
REMARK 465 LYS A 190
REMARK 465 THR A 191
REMARK 465 ASP A 209
REMARK 465 LEU A 210
REMARK 465 ILE A 211
REMARK 465 ALA A 212
REMARK 465 LEU A 213
REMARK 465 GLU A 214
REMARK 465 GLU A 215
REMARK 465 GLU A 216
REMARK 465 LYS A 217
REMARK 465 LYS A 218
REMARK 465 LYS A 219
REMARK 465 GLU A 220
REMARK 465 LYS A 221
REMARK 465 GLU A 222
REMARK 465 LYS A 223
REMARK 465 PRO A 224
REMARK 465 LEU A 225
REMARK 465 MET A 226
REMARK 465 SER A 227
REMARK 465 LYS A 228
REMARK 465 LYS A 229
REMARK 465 LYS A 230
REMARK 465 SER A 231
REMARK 465 HIS A 232
REMARK 465 HIS A 233
REMARK 465 HIS A 234
REMARK 465 LYS A 674
REMARK 465 ASN A 675
REMARK 465 ALA A 676
REMARK 465 LYS A 704
REMARK 465 ASN A 705
REMARK 465 LYS A 706
REMARK 465 PRO A 707
REMARK 465 MET A 708
REMARK 465 GLY A 709
REMARK 465 LEU A 710
REMARK 465 LYS A 711
REMARK 465 ALA B 7
REMARK 465 ARG B 8
REMARK 465 LYS B 9
REMARK 465 SER B 10
REMARK 465 THR B 11
REMARK 465 GLY B 12
REMARK 465 GLY B 13
REMARK 465 LYS B 14
REMARK 465 ALA B 15
REMARK 465 ALA C 1
REMARK 465 ARG C 2
REMARK 465 THR C 3
REMARK 465 GLY C 12
REMARK 465 GLY C 13
REMARK 465 LYS C 14
REMARK 465 ALA C 15
REMARK 465 PRO C 16
REMARK 465 ARG C 17
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 O HOH A 108 O HOH A 154 1.83
REMARK 500 O HOH A 114 O HOH A 159 1.85
REMARK 500 O HOH A 771 O HOH A 783 1.92
REMARK 500 O HOH A 157 O HOH C 174 1.92
REMARK 500 O HOH A 68 O HOH A 80 1.92
REMARK 500 O HOH A 42 O HOH A 772 1.93
REMARK 500 OH TYR A 461 O HOH A 48 1.93
REMARK 500 O HOH A 143 O HOH A 183 1.95
REMARK 500 OD1 ASP A 429 O HOH A 787 1.95
REMARK 500 O HOH A 789 O HOH A 790 1.97
REMARK 500 O HOH A 723 O HOH A 742 2.03
REMARK 500 OE2 GLU A 267 O HOH A 753 2.04
REMARK 500 O HOH A 734 O HOH A 738 2.04
REMARK 500 OH TYR A 527 O HOH A 743 2.09
REMARK 500 O LYS A 685 O HOH A 152 2.09
REMARK 500 O HOH A 105 O HOH A 788 2.09
REMARK 500 O HOH A 30 O HOH A 95 2.10
REMARK 500 O HOH A 797 O HOH A 802 2.12
REMARK 500 NH2 ARG A 341 O HOH A 162 2.13
REMARK 500 O GLN A 248 O HOH A 773 2.13
REMARK 500 O GLU A 604 O HOH A 799 2.15
REMARK 500 O HOH A 34 O HOH A 107 2.16
REMARK 500 O HOH A 140 O HOH A 720 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 67 O HOH A 757 3645 2.11
REMARK 500 O HOH A 112 O HOH A 121 3545 2.18
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 VAL A 275 CB - CA - C ANGL. DEV. = -12.4 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 ASP A 238 -145.86 61.04
REMARK 500 SER A 246 -64.53 -102.90
REMARK 500 VAL A 275 -16.04 89.75
REMARK 500 TYR A 284 152.86 -46.84
REMARK 500 PRO A 289 -7.40 -58.47
REMARK 500 PRO A 371 155.57 -47.87
REMARK 500 ASP A 412 86.20 -65.42
REMARK 500 PRO A 440 151.39 -48.71
REMARK 500 TRP A 453 64.97 -117.64
REMARK 500 ASP A 455 53.54 -91.71
REMARK 500 GLU A 468 38.37 -86.97
REMARK 500 GLU A 604 -88.14 -91.37
REMARK 500 GLU A 638 -161.70 -101.91
REMARK 500 SER A 640 110.09 -32.82
REMARK 500 GLU A 646 35.60 -148.85
REMARK 500 PRO A 672 -178.07 -66.38
REMARK 500 ASN A 702 -8.25 -50.27
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 FE2 A 1 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 OGA A 4 O2'
REMARK 620 2 OGA A 4 O2 81.9
REMARK 620 3 HOH A 7 O 86.4 82.2
REMARK 620 4 HIS A 495 NE2 89.5 170.7 93.8
REMARK 620 5 ASP A 497 OD2 171.7 89.9 93.3 98.7
REMARK 620 6 HIS A 567 NE2 87.8 93.7 173.3 89.5 92.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 2 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 198 SG
REMARK 620 2 CYS A 201 SG 113.5
REMARK 620 3 HIS A 252 ND1 105.7 99.8
REMARK 620 4 CYS A 255 SG 105.5 115.3 117.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 3 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 244 SG
REMARK 620 2 CYS A 247 SG 108.3
REMARK 620 3 CYS A 271 SG 106.8 113.3
REMARK 620 4 CYS A 274 SG 106.7 114.2 107.1
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 FE2 A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 4
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3N9L RELATED DB: PDB
REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND NOG
REMARK 900 RELATED ID: 3N9M RELATED DB: PDB
REMARK 900 APO LYSINE DEMETHYLASE
REMARK 900 RELATED ID: 3N9N RELATED DB: PDB
REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K9ME2) AND NOG
REMARK 900 RELATED ID: 3N9P RELATED DB: PDB
REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K27ME2) AND NOG
REMARK 900 RELATED ID: 3N9Q RELATED DB: PDB
REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND HISTONE H3(K27ME2)
REMARK 900 AND NOG
DBREF 3N9O A 188 711 UNP Q9GYI0 Q9GYI0_CAEEL 201 724
DBREF 3N9O B 1 15 UNP P08898 H3_CAEEL 2 16
DBREF 3N9O C 1 17 UNP P08898 H3_CAEEL 2 18
SEQADV 3N9O GLU A 184 UNP Q9GYI0 EXPRESSION TAG
SEQADV 3N9O PHE A 185 UNP Q9GYI0 EXPRESSION TAG
SEQADV 3N9O HIS A 186 UNP Q9GYI0 EXPRESSION TAG
SEQADV 3N9O MET A 187 UNP Q9GYI0 EXPRESSION TAG
SEQRES 1 A 528 GLU PHE HIS MET GLU GLN LYS THR PRO LYS GLU SER ASP
SEQRES 2 A 528 ARG CYS GLY GLY CYS GLY LYS PHE THR HIS GLU ASP ASP
SEQRES 3 A 528 LEU ILE ALA LEU GLU GLU GLU LYS LYS LYS GLU LYS GLU
SEQRES 4 A 528 LYS PRO LEU MET SER LYS LYS LYS SER HIS HIS HIS LYS
SEQRES 5 A 528 LYS ASN ASP PHE GLN TRP ILE GLY CYS ASP SER CYS GLN
SEQRES 6 A 528 THR TRP TYR HIS PHE LEU CYS SER GLY LEU GLU GLN PHE
SEQRES 7 A 528 GLU TYR TYR LEU TYR GLU LYS PHE PHE CYS PRO LYS CYS
SEQRES 8 A 528 VAL PRO HIS THR GLY HIS SER ILE ARG TYR LYS VAL VAL
SEQRES 9 A 528 ALA PRO HIS ARG TYR ARG TRP TYR SER PRO ASN GLU LYS
SEQRES 10 A 528 HIS LEU GLY ILE GLU VAL GLY SER LYS THR TRP ILE GLU
SEQRES 11 A 528 ASP PHE ILE THR ARG GLU ASN THR VAL PRO SER PRO THR
SEQRES 12 A 528 ASP ASP GLU VAL CYS ILE VAL GLU ASP GLY TYR GLU PHE
SEQRES 13 A 528 ARG ARG GLU PHE GLU LYS LEU GLY GLY ALA ASP ASN TRP
SEQRES 14 A 528 GLY LYS VAL PHE MET VAL LYS ASP MET ASP GLY LEU ASN
SEQRES 15 A 528 MET THR MET PRO LYS PRO GLY PHE ASP LEU GLU ASP VAL
SEQRES 16 A 528 VAL LYS ILE MET GLY SER ASP TYR GLU VAL ASP THR ILE
SEQRES 17 A 528 ASP VAL TYR ASN GLN SER THR TYR SER MET LYS LEU ASP
SEQRES 18 A 528 THR PHE ARG LYS LEU PHE ARG ASP THR LYS ASN ARG PRO
SEQRES 19 A 528 LEU LEU TYR ASN PHE LEU SER LEU GLU PHE SER ASP ASN
SEQRES 20 A 528 ASN GLU MET LYS GLU ILE ALA LYS PRO PRO ARG PHE VAL
SEQRES 21 A 528 GLN GLU ILE SER MET VAL ASN ARG LEU TRP PRO ASP VAL
SEQRES 22 A 528 SER GLY ALA GLU TYR ILE LYS LEU LEU GLN ARG GLU GLU
SEQRES 23 A 528 TYR LEU PRO GLU ASP GLN ARG PRO LYS VAL GLU GLN PHE
SEQRES 24 A 528 CYS LEU ALA GLY MET ALA GLY SER TYR THR ASP PHE HIS
SEQRES 25 A 528 VAL ASP PHE GLY GLY SER SER VAL TYR TYR HIS ILE LEU
SEQRES 26 A 528 LYS GLY GLU LYS ILE PHE TYR ILE ALA ALA PRO THR GLU
SEQRES 27 A 528 GLN ASN PHE ALA ALA TYR GLN ALA HIS GLU THR SER PRO
SEQRES 28 A 528 ASP THR THR THR TRP PHE GLY ASP ILE ALA ASN GLY ALA
SEQRES 29 A 528 VAL LYS ARG VAL VAL ILE LYS GLU GLY GLN THR LEU LEU
SEQRES 30 A 528 ILE PRO ALA GLY TRP ILE HIS ALA VAL LEU THR PRO VAL
SEQRES 31 A 528 ASP SER LEU VAL PHE GLY GLY ASN PHE LEU HIS LEU GLY
SEQRES 32 A 528 ASN LEU GLU MET GLN MET ARG VAL TYR HIS LEU GLU ASN
SEQRES 33 A 528 ALA ILE ARG LYS GLU ILE ARG SER GLU GLU LYS PHE TYR
SEQRES 34 A 528 PHE PRO ASN PHE GLU LEU LEU HIS TRP MET TYR MET ARG
SEQRES 35 A 528 ASN VAL LEU LEU GLU LYS ILE THR GLU ALA ASN GLN GLU
SEQRES 36 A 528 GLY SER ASP MET ARG GLU GLN GLU LYS ASN ILE TRP THR
SEQRES 37 A 528 ALA SER GLN ILE MET LYS ALA GLU MET GLU ARG TRP MET
SEQRES 38 A 528 ASP ARG GLU LEU ARG LEU GLY PRO GLU LYS ASN ALA ILE
SEQRES 39 A 528 LEU PRO THR ASP ASP LYS ASN LYS ILE MET ILE SER VAL
SEQRES 40 A 528 ARG LYS GLN ILE GLU ILE GLN THR LYS ILE GLN ASN ALA
SEQRES 41 A 528 LYS ASN LYS PRO MET GLY LEU LYS
SEQRES 1 B 15 ALA ARG THR M3L GLN THR ALA ARG LYS SER THR GLY GLY
SEQRES 2 B 15 LYS ALA
SEQRES 1 C 17 ALA ARG THR LYS GLN THR ALA ARG MLY SER THR GLY GLY
SEQRES 2 C 17 LYS ALA PRO ARG
MODRES 3N9O M3L B 4 LYS N-TRIMETHYLLYSINE
MODRES 3N9O MLY C 9 LYS N-DIMETHYL-LYSINE
HET M3L B 4 12
HET MLY C 9 11
HET FE2 A 1 1
HET ZN A 2 1
HET ZN A 3 1
HET OGA A 4 10
HETNAM M3L N-TRIMETHYLLYSINE
HETNAM MLY N-DIMETHYL-LYSINE
HETNAM FE2 FE (II) ION
HETNAM ZN ZINC ION
HETNAM OGA N-OXALYLGLYCINE
FORMUL 2 M3L C9 H21 N2 O2 1+
FORMUL 3 MLY C8 H18 N2 O2
FORMUL 4 FE2 FE 2+
FORMUL 5 ZN 2(ZN 2+)
FORMUL 7 OGA C4 H5 N O5
FORMUL 8 HOH *277(H2 O)
HELIX 1 1 LYS A 193 ARG A 197 5 5
HELIX 2 2 LEU A 254 SER A 256 5 3
HELIX 3 3 GLU A 259 TYR A 263 5 5
HELIX 4 4 SER A 296 LYS A 300 5 5
HELIX 5 5 SER A 308 THR A 317 1 10
HELIX 6 6 ARG A 318 VAL A 322 5 5
HELIX 7 7 GLY A 336 LEU A 346 1 11
HELIX 8 8 GLY A 347 TRP A 352 5 6
HELIX 9 9 ASP A 374 GLY A 383 1 10
HELIX 10 10 LEU A 403 ASP A 412 1 10
HELIX 11 11 GLU A 432 ALA A 437 1 6
HELIX 12 12 PRO A 440 SER A 447 1 8
HELIX 13 13 SER A 447 TRP A 453 1 7
HELIX 14 14 SER A 457 ARG A 467 1 11
HELIX 15 15 PRO A 472 ARG A 476 5 5
HELIX 16 16 ASP A 497 SER A 501 5 5
HELIX 17 17 THR A 520 SER A 533 1 14
HELIX 18 18 TRP A 539 ALA A 544 1 6
HELIX 19 19 HIS A 584 GLY A 586 5 3
HELIX 20 20 ASN A 587 ILE A 605 1 19
HELIX 21 21 GLU A 608 TYR A 612 5 5
HELIX 22 22 ASN A 615 VAL A 627 1 13
HELIX 23 23 VAL A 627 GLU A 638 1 12
HELIX 24 24 GLU A 646 GLY A 671 1 26
HELIX 25 25 PRO A 679 ALA A 703 1 25
SHEET 1 A 3 TRP A 250 HIS A 252 0
SHEET 2 A 3 GLN A 240 GLY A 243 -1 N ILE A 242 O TYR A 251
SHEET 3 A 3 THR B 3 GLN B 5 -1 O M3L B 4 N TRP A 241
SHEET 1 B 2 TYR A 266 LYS A 268 0
SHEET 2 B 2 ILE A 282 ARG A 283 -1 O ILE A 282 N GLU A 267
SHEET 1 C 6 VAL A 330 ASP A 335 0
SHEET 2 C 6 VAL A 355 ASP A 360 1 O MET A 357 N VAL A 333
SHEET 3 C 6 THR A 558 ILE A 561 -1 O LEU A 560 N PHE A 356
SHEET 4 C 6 SER A 502 ALA A 517 -1 N TYR A 505 O LEU A 559
SHEET 5 C 6 ILE A 566 PHE A 582 -1 O PHE A 582 N SER A 502
SHEET 6 C 6 SER A 490 HIS A 495 -1 N THR A 492 O VAL A 569
SHEET 1 D 7 SER A 397 LYS A 402 0
SHEET 2 D 7 GLU A 387 ASP A 392 -1 N THR A 390 O TYR A 399
SHEET 3 D 7 TYR A 420 GLU A 426 -1 O ASN A 421 N ILE A 391
SHEET 4 D 7 PHE A 482 GLY A 486 -1 O ALA A 485 N PHE A 422
SHEET 5 D 7 ILE A 566 PHE A 582 -1 O GLY A 579 N PHE A 482
SHEET 6 D 7 SER A 502 ALA A 517 -1 N SER A 502 O PHE A 582
SHEET 7 D 7 LYS A 549 LYS A 554 -1 O ILE A 553 N LYS A 512
LINK C THR B 3 N M3L B 4 1555 1555 1.33
LINK C M3L B 4 N GLN B 5 1555 1555 1.33
LINK C ARG C 8 N MLY C 9 1555 1555 1.33
LINK C MLY C 9 N SER C 10 1555 1555 1.33
LINK FE FE2 A 1 O2' OGA A 4 1555 1555 2.19
LINK FE FE2 A 1 O2 OGA A 4 1555 1555 2.25
LINK FE FE2 A 1 O HOH A 7 1555 1555 2.24
LINK FE FE2 A 1 NE2 HIS A 495 1555 1555 2.13
LINK FE FE2 A 1 OD2 ASP A 497 1555 1555 2.14
LINK FE FE2 A 1 NE2 HIS A 567 1555 1555 2.15
LINK ZN ZN A 2 SG CYS A 198 1555 1555 2.36
LINK ZN ZN A 2 SG CYS A 201 1555 1555 2.34
LINK ZN ZN A 2 ND1 HIS A 252 1555 1555 2.27
LINK ZN ZN A 2 SG CYS A 255 1555 1555 2.34
LINK ZN ZN A 3 SG CYS A 244 1555 1555 2.35
LINK ZN ZN A 3 SG CYS A 247 1555 1555 2.33
LINK ZN ZN A 3 SG CYS A 271 1555 1555 2.63
LINK ZN ZN A 3 SG CYS A 274 1555 1555 2.37
SITE 1 AC1 5 OGA A 4 HOH A 7 HIS A 495 ASP A 497
SITE 2 AC1 5 HIS A 567
SITE 1 AC2 4 CYS A 198 CYS A 201 HIS A 252 CYS A 255
SITE 1 AC3 4 CYS A 244 CYS A 247 CYS A 271 CYS A 274
SITE 1 AC4 13 FE2 A 1 HOH A 7 HOH A 33 ASN A 421
SITE 2 AC4 13 LEU A 423 THR A 492 HIS A 495 ASP A 497
SITE 3 AC4 13 TYR A 505 LYS A 512 HIS A 567 VAL A 569
SITE 4 AC4 13 MLY C 9
CRYST1 69.090 87.379 102.727 90.00 90.00 90.00 P 21 21 21 4
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 0.014474 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011444 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009735 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
