HEADER OXIDOREDUCTASE 07-FEB-17 5PHI
TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D IN
TITLE 2 COMPLEX WITH N09480A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D,
COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2D;
COMPND 6 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: KDM4D, JHDM3D, JMJD2D;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, JMJ DOMAIN,
KEYWDS 2 EPIGENETICS, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR N.M.PEARCE,T.KROJER,R.TALON,A.R.BRADLEY,M.FAIRHEAD,R.SETHI,N.WRIGHT,
AUTHOR 2 E.MACLEAN,P.COLLINS,J.BRANDAO-NETO,A.DOUANGAMATH,Z.RENJIE,A.DIAS,
AUTHOR 3 M.VOLLMAR,J.NG,A.SZYKOWSKA,N.BURGESS-BROWN,P.E.BRENNAN,O.COX,
AUTHOR 4 U.OPPERMANN,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT
REVDAT 4 06-MAR-24 5PHI 1 REMARK
REVDAT 3 04-OCT-17 5PHI 1 REMARK
REVDAT 2 27-SEP-17 5PHI 1 JRNL REMARK
REVDAT 1 15-MAR-17 5PHI 0
JRNL AUTH N.M.PEARCE,T.KROJER,A.R.BRADLEY,P.COLLINS,R.P.NOWAK,R.TALON,
JRNL AUTH 2 B.D.MARSDEN,S.KELM,J.SHI,C.M.DEANE,F.VON DELFT
JRNL TITL A MULTI-CRYSTAL METHOD FOR EXTRACTING OBSCURED
JRNL TITL 2 CRYSTALLOGRAPHIC STATES FROM CONVENTIONALLY UNINTERPRETABLE
JRNL TITL 3 ELECTRON DENSITY.
JRNL REF NAT COMMUN V. 8 15123 2017
JRNL REFN ESSN 2041-1723
JRNL PMID 28436492
JRNL DOI 10.1038/NCOMMS15123
REMARK 2
REMARK 2 RESOLUTION. 1.97 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1682
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) : 1.97
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 28264
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.160
REMARK 3 R VALUE (WORKING SET) : 0.157
REMARK 3 FREE R VALUE : 0.219
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710
REMARK 3 FREE R VALUE TEST SET COUNT : 1331
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 29.4525 - 4.2427 1.00 2933 137 0.1650 0.2089
REMARK 3 2 4.2427 - 3.3691 1.00 2769 134 0.1352 0.1821
REMARK 3 3 3.3691 - 2.9437 1.00 2716 151 0.1440 0.2151
REMARK 3 4 2.9437 - 2.6747 1.00 2686 141 0.1517 0.2327
REMARK 3 5 2.6747 - 2.4831 1.00 2685 142 0.1598 0.2227
REMARK 3 6 2.4831 - 2.3368 1.00 2668 133 0.1641 0.2423
REMARK 3 7 2.3368 - 2.2198 1.00 2661 138 0.1622 0.2960
REMARK 3 8 2.2198 - 2.1232 1.00 2688 105 0.1706 0.2171
REMARK 3 9 2.1232 - 2.0415 1.00 2657 123 0.1817 0.2172
REMARK 3 10 2.0415 - 1.9711 0.93 2470 127 0.2173 0.2963
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 : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.690
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 25.48
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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 : 0.008 3092
REMARK 3 ANGLE : 1.177 4229
REMARK 3 CHIRALITY : 0.049 413
REMARK 3 PLANARITY : 0.009 561
REMARK 3 DIHEDRAL : 13.997 1164
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 5PHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-17.
REMARK 100 THE DEPOSITION ID IS D_1001400666.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-DEC-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I03
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28332
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970
REMARK 200 RESOLUTION RANGE LOW (A) : 29.449
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 12.70
REMARK 200 R MERGE (I) : 0.09700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8
REMARK 200 DATA REDUNDANCY IN SHELL : 10.90
REMARK 200 R MERGE FOR SHELL (I) : 0.90500
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: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: REFMAC
REMARK 200 STARTING MODEL: 4D6R
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG3350 -- 0.1M HEPES PH 7.0 --
REMARK 280 0.25M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.39500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.76650
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.76650
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.09250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.76650
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.76650
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.69750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.76650
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.76650
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.09250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.76650
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.76650
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.69750
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.39500
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: MONOMERIC
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 723 LIES ON A SPECIAL POSITION.
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 MET A -21
REMARK 465 HIS A -20
REMARK 465 HIS A -19
REMARK 465 HIS A -18
REMARK 465 HIS A -17
REMARK 465 HIS A -16
REMARK 465 HIS A -15
REMARK 465 SER A -14
REMARK 465 SER A -13
REMARK 465 GLY A -12
REMARK 465 VAL A -11
REMARK 465 ASP A -10
REMARK 465 LEU A -9
REMARK 465 GLY A -8
REMARK 465 THR A -7
REMARK 465 GLU A -6
REMARK 465 ASN A -5
REMARK 465 LEU A -4
REMARK 465 TYR A -3
REMARK 465 PHE A -2
REMARK 465 GLN A -1
REMARK 465 SER A 0
REMARK 465 MET A 1
REMARK 465 GLU A 2
REMARK 465 THR A 3
REMARK 465 MET A 4
REMARK 465 LYS A 5
REMARK 465 SER A 6
REMARK 465 LYS A 7
REMARK 465 ALA A 8
REMARK 465 ASN A 9
REMARK 465 CYS A 10
REMARK 465 ARG A 338
REMARK 465 GLY A 339
REMARK 465 GLN A 340
REMARK 465 ASP A 341
REMARK 465 ARG A 342
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 LYS A 58 CG CD CE NZ
REMARK 470 GLU A 61 CG CD OE1 OE2
REMARK 470 LYS A 92 NZ
REMARK 470 ARG A 225 NE CZ NH1 NH2
REMARK 470 LYS A 255 CD CE NZ
REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 337 CG CD 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 O HOH A 611 O HOH A 730 2.01
REMARK 500 O1 SO4 A 411 O HOH A 501 2.02
REMARK 500 O HOH A 559 O HOH A 706 2.05
REMARK 500 O HOH A 702 O HOH A 754 2.07
REMARK 500 O HOH A 705 O HOH A 724 2.08
REMARK 500 O HOH A 784 O HOH A 786 2.08
REMARK 500 O HOH A 757 O HOH A 793 2.09
REMARK 500 O HOH A 718 O HOH A 745 2.09
REMARK 500 O1 EDO A 404 O HOH A 502 2.11
REMARK 500 O PHE A 319 O HOH A 503 2.11
REMARK 500 O HOH A 730 O HOH A 782 2.12
REMARK 500 O HOH A 521 O HOH A 743 2.13
REMARK 500 O HOH A 646 O HOH A 781 2.14
REMARK 500 O HOH A 645 O HOH A 737 2.16
REMARK 500 O HOH A 624 O HOH A 791 2.17
REMARK 500 O HOH A 778 O HOH A 780 2.17
REMARK 500 O HOH A 543 O HOH A 628 2.17
REMARK 500 O HOH A 611 O HOH A 782 2.18
REMARK 500 O HOH A 627 O HOH A 718 2.18
REMARK 500 O HOH A 698 O HOH A 738 2.18
REMARK 500 OE2 GLU A 331 O HOH A 504 2.18
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 501 O HOH A 571 6555 2.12
REMARK 500 O HOH A 570 O HOH A 678 6445 2.19
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 ASN A 65 45.97 -109.10
REMARK 500 LYS A 186 -4.28 73.82
REMARK 500 ASP A 197 39.88 38.57
REMARK 500 ASP A 197 39.88 39.50
REMARK 500 ALA A 240 52.03 -143.89
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 ASP A 195 -11.78
REMARK 500 ASP A 195 -12.99
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 <JMJD2DA-X568> <USED_FOR_STATISTICAL_MAP>YES</USED_FOR_STATISTICAL_
REMARK 600 MAP> <SMILES_OF_COMPOUND_ADDED>CC1NC2CCCCC2[NH]1</SMILES_OF_
REMARK 600 COMPOUND_ADDED> <SITE8> <LABEL>NONE</LABEL> <COORDINATE>8.46 6.85
REMARK 600 6.85</COORDINATE> <SMILES>CC1NC2CCCCC2[NH]1</SMILES> <CONFIDENCE>4 -
REMARK 600 HIGH CONFIDENCE</CONFIDENCE> <COMMENT>NONE</COMMENT> <OCCUPANCY>
REMARK 600 0.52</OCCUPANCY> <B_AVERAGE>28.103</B_AVERAGE> <B_RATIO>
REMARK 600 1.1533836499669619</B_RATIO> <RSCC>0.83199999999999996</RSCC> <RSR>
REMARK 600 0.124</RSR> <RSZD>1.0</RSZD> <RMSD>0.27087395592784475</RMSD> </
REMARK 600 SITE8> </JMJD2DA-X568>
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 NI A 402 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 192 NE2
REMARK 620 2 GLU A 194 OE1 98.2
REMARK 620 3 HIS A 280 NE2 85.0 87.4
REMARK 620 4 OGA A 403 O1 170.0 91.7 94.1
REMARK 620 5 OGA A 403 O2' 92.5 168.4 98.0 77.8
REMARK 620 6 HOH A 526 O 89.9 91.4 174.5 91.3 84.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 401 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 238 SG
REMARK 620 2 HIS A 244 NE2 111.8
REMARK 620 3 CYS A 310 SG 116.7 107.1
REMARK 620 4 CYS A 312 SG 115.8 99.2 104.5
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 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 411
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 413
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 414
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 415
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8P7 A 416
DBREF 5PHI A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342
SEQADV 5PHI MET A -21 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI HIS A -20 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI HIS A -19 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI HIS A -18 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI HIS A -17 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI HIS A -16 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI HIS A -15 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI SER A -14 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI SER A -13 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI GLY A -12 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI VAL A -11 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI ASP A -10 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI LEU A -9 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI GLY A -8 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI THR A -7 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI GLU A -6 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI ASN A -5 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI LEU A -4 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI TYR A -3 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI PHE A -2 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI GLN A -1 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5PHI SER A 0 UNP Q6B0I6 EXPRESSION TAG
SEQRES 1 A 364 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU
SEQRES 2 A 364 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLU THR MET
SEQRES 3 A 364 LYS SER LYS ALA ASN CYS ALA GLN ASN PRO ASN CYS ASN
SEQRES 4 A 364 ILE MET ILE PHE HIS PRO THR LYS GLU GLU PHE ASN ASP
SEQRES 5 A 364 PHE ASP LYS TYR ILE ALA TYR MET GLU SER GLN GLY ALA
SEQRES 6 A 364 HIS ARG ALA GLY LEU ALA LYS ILE ILE PRO PRO LYS GLU
SEQRES 7 A 364 TRP LYS ALA ARG GLU THR TYR ASP ASN ILE SER GLU ILE
SEQRES 8 A 364 LEU ILE ALA THR PRO LEU GLN GLN VAL ALA SER GLY ARG
SEQRES 9 A 364 ALA GLY VAL PHE THR GLN TYR HIS LYS LYS LYS LYS ALA
SEQRES 10 A 364 MET THR VAL GLY GLU TYR ARG HIS LEU ALA ASN SER LYS
SEQRES 11 A 364 LYS TYR GLN THR PRO PRO HIS GLN ASN PHE GLU ASP LEU
SEQRES 12 A 364 GLU ARG LYS TYR TRP LYS ASN ARG ILE TYR ASN SER PRO
SEQRES 13 A 364 ILE TYR GLY ALA ASP ILE SER GLY SER LEU PHE ASP GLU
SEQRES 14 A 364 ASN THR LYS GLN TRP ASN LEU GLY HIS LEU GLY THR ILE
SEQRES 15 A 364 GLN ASP LEU LEU GLU LYS GLU CYS GLY VAL VAL ILE GLU
SEQRES 16 A 364 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS
SEQRES 17 A 364 THR THR PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR
SEQRES 18 A 364 SER ILE ASN TYR LEU HIS LEU GLY GLU PRO LYS THR TRP
SEQRES 19 A 364 TYR VAL VAL PRO PRO GLU HIS GLY GLN ARG LEU GLU ARG
SEQRES 20 A 364 LEU ALA ARG GLU LEU PHE PRO GLY SER SER ARG GLY CYS
SEQRES 21 A 364 GLY ALA PHE LEU ARG HIS LYS VAL ALA LEU ILE SER PRO
SEQRES 22 A 364 THR VAL LEU LYS GLU ASN GLY ILE PRO PHE ASN ARG ILE
SEQRES 23 A 364 THR GLN GLU ALA GLY GLU PHE MET VAL THR PHE PRO TYR
SEQRES 24 A 364 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA
SEQRES 25 A 364 GLU ALA ILE ASN PHE ALA THR PRO ARG TRP ILE ASP TYR
SEQRES 26 A 364 GLY LYS MET ALA SER GLN CYS SER CYS GLY GLU ALA ARG
SEQRES 27 A 364 VAL THR PHE SER MET ASP ALA PHE VAL ARG ILE LEU GLN
SEQRES 28 A 364 PRO GLU ARG TYR ASP LEU TRP LYS ARG GLY GLN ASP ARG
HET ZN A 401 1
HET NI A 402 1
HET OGA A 403 10
HET EDO A 404 4
HET EDO A 405 4
HET EDO A 406 4
HET EDO A 407 4
HET EDO A 408 4
HET EDO A 409 4
HET EDO A 410 4
HET SO4 A 411 5
HET SO4 A 412 5
HET SO4 A 413 5
HET SO4 A 414 5
HET SO4 A 415 5
HET 8P7 A 416 10
HETNAM ZN ZINC ION
HETNAM NI NICKEL (II) ION
HETNAM OGA N-OXALYLGLYCINE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM SO4 SULFATE ION
HETNAM 8P7 2-METHYL-1~{H}-BENZIMIDAZOLE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN ZN 2+
FORMUL 3 NI NI 2+
FORMUL 4 OGA C4 H5 N O5
FORMUL 5 EDO 7(C2 H6 O2)
FORMUL 12 SO4 5(O4 S 2-)
FORMUL 17 8P7 C8 H8 N2
FORMUL 18 HOH *306(H2 O)
HELIX 1 AA1 GLU A 26 ASN A 29 5 4
HELIX 2 AA2 ASP A 30 GLN A 41 1 12
HELIX 3 AA3 GLY A 42 ALA A 46 5 5
HELIX 4 AA4 VAL A 98 ASN A 106 1 9
HELIX 5 AA5 ASN A 117 ARG A 129 1 13
HELIX 6 AA6 ILE A 130 ASN A 132 5 3
HELIX 7 AA7 THR A 159 GLY A 169 1 11
HELIX 8 AA8 GLU A 194 LEU A 198 5 5
HELIX 9 AA9 PRO A 216 GLU A 218 5 3
HELIX 10 AB1 HIS A 219 PHE A 231 1 13
HELIX 11 AB2 PHE A 231 CYS A 238 1 8
HELIX 12 AB3 ALA A 240 LYS A 245 5 6
HELIX 13 AB4 SER A 250 ASN A 257 1 8
HELIX 14 AB5 ARG A 299 ALA A 307 1 9
HELIX 15 AB6 THR A 318 GLN A 329 1 12
HELIX 16 AB7 GLN A 329 LYS A 337 1 9
SHEET 1 AA110 MET A 19 PHE A 21 0
SHEET 2 AA110 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21
SHEET 3 AA110 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51
SHEET 4 AA110 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272
SHEET 5 AA110 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203
SHEET 6 AA110 TYR A 179 GLY A 183 -1 N TYR A 181 O ALA A 290
SHEET 7 AA110 ILE A 135 SER A 141 -1 N ILE A 140 O LEU A 180
SHEET 8 AA110 LEU A 75 GLY A 81 -1 N LEU A 75 O TYR A 136
SHEET 9 AA110 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76
SHEET 10 AA110 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86
SHEET 1 AA2 2 LEU A 70 ILE A 71 0
SHEET 2 AA2 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71
SHEET 1 AA3 4 THR A 188 HIS A 192 0
SHEET 2 AA3 4 TYR A 279 ASN A 284 -1 O GLY A 282 N PHE A 189
SHEET 3 AA3 4 LYS A 210 VAL A 215 -1 N TYR A 213 O ALA A 281
SHEET 4 AA3 4 ASN A 262 GLN A 266 -1 O ILE A 264 N TRP A 212
LINK NE2 HIS A 192 NI NI A 402 1555 1555 2.29
LINK OE1 GLU A 194 NI NI A 402 1555 1555 2.12
LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.13
LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.08
LINK NE2 HIS A 280 NI NI A 402 1555 1555 2.20
LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.30
LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.41
LINK NI NI A 402 O1 OGA A 403 1555 1555 2.13
LINK NI NI A 402 O2' OGA A 403 1555 1555 2.13
LINK NI NI A 402 O HOH A 526 1555 1555 2.10
SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312
SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 OGA A 403
SITE 2 AC2 5 HOH A 526
SITE 1 AC3 12 TYR A 136 PHE A 189 HIS A 192 GLU A 194
SITE 2 AC3 12 SER A 200 ASN A 202 LYS A 210 HIS A 280
SITE 3 AC3 12 NI A 402 EDO A 410 HOH A 526 HOH A 666
SITE 1 AC4 8 LYS A 150 GLN A 151 TRP A 152 ASN A 153
SITE 2 AC4 8 HIS A 156 LEU A 157 HOH A 502 HOH A 689
SITE 1 AC5 4 PRO A 251 LYS A 255 ARG A 263 HOH A 539
SITE 1 AC6 8 GLU A 224 ALA A 240 PHE A 241 LEU A 242
SITE 2 AC6 8 TYR A 279 SER A 308 HOH A 521 HOH A 553
SITE 1 AC7 6 PHE A 118 THR A 211 ARG A 263 THR A 265
SITE 2 AC7 6 SO4 A 414 HOH A 527
SITE 1 AC8 5 LYS A 58 ALA A 59 TYR A 203 HOH A 542
SITE 2 AC8 5 HOH A 563
SITE 1 AC9 6 SER A 80 THR A 87 CYS A 168 LYS A 305
SITE 2 AC9 6 HOH A 518 HOH A 591
SITE 1 AD1 5 TYR A 181 SER A 200 ASN A 294 OGA A 403
SITE 2 AD1 5 HOH A 526
SITE 1 AD2 5 ARG A 102 HIS A 103 ASN A 106 HOH A 501
SITE 2 AD2 5 HOH A 654
SITE 1 AD3 7 ARG A 60 GLU A 61 THR A 62 HOH A 509
SITE 2 AD3 7 HOH A 517 HOH A 554 HOH A 680
SITE 1 AD4 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128
SITE 1 AD5 9 PHE A 118 ARG A 263 ILE A 264 THR A 265
SITE 2 AD5 9 EDO A 407 8P7 A 416 HOH A 527 HOH A 585
SITE 3 AD5 9 HOH A 734
SITE 1 AD6 5 PRO A 113 LYS A 124 ASN A 128 TRP A 185
SITE 2 AD6 5 LYS A 186
SITE 1 AD7 5 PHE A 118 THR A 265 GLU A 267 SO4 A 414
SITE 2 AD7 5 HOH A 734
CRYST1 71.533 71.533 150.790 90.00 90.00 90.00 P 43 21 2 8
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 0.013980 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013980 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006632 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
