HEADER OXIDOREDUCTASE 02-FEB-16 5FV3 TITLE CRYSTAL STRUCTURE OF HUMAN JARID1B CONSTRUCT C2 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 26-101, JMJC DOMAIN, RESIDUES 374- COMPND 6 770; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, JARID1B, PLU1 EXPDTA X-RAY DIFFRACTION AUTHOR R.NOWAK,V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,K.KUPINSKA,C.STRAIN- AUTHOR 2 DAMERELL,A.SZYKOWSKA,R.TALON,F.VON DELFT,N.A.BURGESS-BROWN, AUTHOR 3 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN REVDAT 6 10-JAN-24 5FV3 1 REMARK LINK REVDAT 5 24-JAN-18 5FV3 1 AUTHOR REVDAT 4 29-JUN-16 5FV3 1 JRNL REVDAT 3 01-JUN-16 5FV3 1 JRNL REVDAT 2 25-MAY-16 5FV3 1 JRNL REVDAT 1 17-FEB-16 5FV3 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. 2.37 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 123.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37476 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1847 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1123.4458 - 5.5727 1.00 2968 170 0.1790 0.2046 REMARK 3 2 5.5727 - 4.4232 1.00 2812 140 0.1364 0.1639 REMARK 3 3 4.4232 - 3.8640 1.00 2762 152 0.1392 0.1770 REMARK 3 4 3.8640 - 3.5107 1.00 2738 159 0.1635 0.2012 REMARK 3 5 3.5107 - 3.2590 1.00 2767 106 0.1938 0.2517 REMARK 3 6 3.2590 - 3.0669 1.00 2721 151 0.2180 0.2673 REMARK 3 7 3.0669 - 2.9133 1.00 2738 122 0.2363 0.2958 REMARK 3 8 2.9133 - 2.7864 1.00 2688 144 0.2550 0.3210 REMARK 3 9 2.7864 - 2.6792 1.00 2688 147 0.2716 0.3489 REMARK 3 10 2.6792 - 2.5867 1.00 2679 148 0.2957 0.3581 REMARK 3 11 2.5867 - 2.5058 1.00 2721 120 0.3008 0.3395 REMARK 3 12 2.5058 - 2.4342 1.00 2681 144 0.3207 0.4126 REMARK 3 13 2.4342 - 2.3701 1.00 2666 144 0.3257 0.3802 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 : 2.00 REMARK 3 B_SOL : 2.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 3894 REMARK 3 ANGLE : 0.703 5283 REMARK 3 CHIRALITY : 0.028 561 REMARK 3 PLANARITY : 0.004 677 REMARK 3 DIHEDRAL : 13.318 1429 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: SIDE CHAINS WITHOUT DENSITY WERE REMARK 3 REMOVED. SOME RESIDUES HAVE ALTERNATIVE CONFORMATION. GLYCINE REMARK 3 LINKER DOES NOT EXIST. REMARK 4 REMARK 4 5FV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1290066165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37525 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 123.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.31000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.20 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE REMARK 200 STARTING MODEL: PDB ENTRY 5A1F REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 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 101.55333 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 50.77667 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 76.16500 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 25.38833 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 126.94167 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 101.55333 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 50.77667 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 25.38833 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 76.16500 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 126.94167 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 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 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 A2100 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 GLY A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 104 REMARK 465 GLY A 105 REMARK 465 GLY A 106 REMARK 465 PHE A 370 REMARK 465 GLU A 371 REMARK 465 GLN A 372 REMARK 465 ALA A 373 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 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 ASP A 69 CG OD1 OD2 REMARK 470 GLN A 71 CG CD OE1 NE2 REMARK 470 ARG A 375 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 417 CG1 CG2 CD1 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 ASP A 420 CG OD1 OD2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 ASP A 442 CG OD1 OD2 REMARK 470 GLU A 468 CG CD OE1 OE2 REMARK 470 GLU A 616 CG CD OE1 OE2 REMARK 470 GLU A 660 CG CD OE1 OE2 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 NZ LYS A 80 O CYS A 723 3665 2.18 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 LEU A 90 76.34 -108.16 REMARK 500 LEU A 93 -2.67 68.07 REMARK 500 GLU A 468 -1.08 67.15 REMARK 500 PHE A 493 -7.20 76.08 REMARK 500 ASP A 547 -166.29 -161.19 REMARK 500 PHE A 700 -53.79 -146.68 REMARK 500 PHE A 700 -51.93 -146.68 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 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 100.4 REMARK 620 3 HIS A 587 NE2 88.5 86.9 REMARK 620 4 OGA A1770 O1 170.9 88.6 92.7 REMARK 620 5 OGA A1770 O2' 90.5 163.7 105.6 80.5 REMARK 620 6 HOH A2054 O 90.3 83.8 170.2 90.0 84.0 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 108.0 REMARK 620 3 CYS A 715 SG 122.4 113.6 REMARK 620 4 HIS A 718 ND1 109.3 101.3 99.7 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 DMS A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS 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 EPE A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1768 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1769 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 1770 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FUP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH 2- OXOGLUTARATE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE REMARK 999 N102 (INCLUDING) TO F368 (INCLUDING) WAS DELETED AND REMARK 999 LINKED BY FOUR GLYCINE RESIDUES (GLYCINE LINKER) DBREF 5FV3 A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5FV3 A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770 SEQADV 5FV3 SER A -1 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FV3 MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FV3 GLY A 102 UNP Q9UGL1 LINKER SEQADV 5FV3 GLY A 103 UNP Q9UGL1 LINKER SEQADV 5FV3 GLY A 104 UNP Q9UGL1 LINKER SEQADV 5FV3 GLY A 105 UNP Q9UGL1 LINKER SEQRES 1 A 484 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 484 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 484 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 484 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 484 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 484 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 484 GLY GLY GLY GLY GLY PHE GLU GLN ALA ALA ARG ASP TYR SEQRES 8 A 484 THR LEU ARG THR PHE GLY GLU MET ALA ASP ALA PHE LYS SEQRES 9 A 484 SER ASP TYR PHE ASN MET PRO VAL HIS MET VAL PRO THR SEQRES 10 A 484 GLU LEU VAL GLU LYS GLU PHE TRP ARG LEU VAL SER THR SEQRES 11 A 484 ILE GLU GLU ASP VAL THR VAL GLU TYR GLY ALA ASP ILE SEQRES 12 A 484 ALA SER LYS GLU PHE GLY SER GLY PHE PRO VAL ARG ASP SEQRES 13 A 484 GLY LYS ILE LYS LEU SER PRO GLU GLU GLU GLU TYR LEU SEQRES 14 A 484 ASP SER GLY TRP ASN LEU ASN ASN MET PRO VAL MET GLU SEQRES 15 A 484 GLN SER VAL LEU ALA HIS ILE THR ALA ASP ILE CYS GLY SEQRES 16 A 484 MET LYS LEU PRO TRP LEU TYR VAL GLY MET CYS PHE SER SEQRES 17 A 484 SER PHE CYS TRP HIS ILE GLU ASP HIS TRP SER TYR SER SEQRES 18 A 484 ILE ASN TYR LEU HIS TRP GLY GLU PRO LYS THR TRP TYR SEQRES 19 A 484 GLY VAL PRO GLY TYR ALA ALA GLU GLN LEU GLU ASN VAL SEQRES 20 A 484 MET LYS LYS LEU ALA PRO GLU LEU PHE VAL SER GLN PRO SEQRES 21 A 484 ASP LEU LEU HIS GLN LEU VAL THR ILE MET ASN PRO ASN SEQRES 22 A 484 THR LEU MET THR HIS GLU VAL PRO VAL TYR ARG THR ASN SEQRES 23 A 484 GLN CYS ALA GLY GLU PHE VAL ILE THR PHE PRO ARG ALA SEQRES 24 A 484 TYR HIS SER GLY PHE ASN GLN GLY PHE ASN PHE ALA GLU SEQRES 25 A 484 ALA VAL ASN PHE CYS THR VAL ASP TRP LEU PRO LEU GLY SEQRES 26 A 484 ARG GLN CYS VAL GLU HIS TYR ARG LEU LEU HIS ARG TYR SEQRES 27 A 484 CYS VAL PHE SER HIS ASP GLU MET ILE CYS LYS MET ALA SEQRES 28 A 484 SER LYS ALA ASP VAL LEU ASP VAL VAL VAL ALA SER THR SEQRES 29 A 484 VAL GLN LYS ASP MET ALA ILE MET ILE GLU ASP GLU LYS SEQRES 30 A 484 ALA LEU ARG GLU THR VAL ARG LYS LEU GLY VAL ILE ASP SEQRES 31 A 484 SER GLU ARG MET ASP PHE GLU LEU LEU PRO ASP ASP GLU SEQRES 32 A 484 ARG GLN CYS VAL LYS CYS LYS THR THR CYS PHE MET SER SEQRES 33 A 484 ALA ILE SER CYS SER CYS LYS PRO GLY LEU LEU VAL CYS SEQRES 34 A 484 LEU HIS HIS VAL LYS GLU LEU CYS SER CYS PRO PRO TYR SEQRES 35 A 484 LYS TYR LYS LEU ARG TYR ARG TYR THR LEU ASP ASP LEU SEQRES 36 A 484 TYR PRO MET MET ASN ALA LEU LYS LEU ARG ALA GLU SER SEQRES 37 A 484 TYR ASN GLU TRP ALA LEU ASN VAL ASN GLU ALA LEU GLU SEQRES 38 A 484 ALA LYS ILE HET ZN A1754 1 HET DMS A1755 4 HET DMS A1756 4 HET MN A1757 1 HET MN A1758 1 HET EPE A1759 15 HET EDO A1760 4 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 HET EDO A1768 4 HET CL A1769 1 HET OGA A1770 10 HETNAM ZN ZINC ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM MN MANGANESE (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM OGA N-OXALYLGLYCINE HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 DMS 2(C2 H6 O S) FORMUL 5 MN 2(MN 2+) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 8 EDO 9(C2 H6 O2) FORMUL 17 CL CL 1- FORMUL 18 OGA C4 H5 N O5 FORMUL 19 HOH *120(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 VAL A 414 1 13 HELIX 6 6 SER A 448 TYR A 454 1 7 HELIX 7 7 ASN A 463 MET A 467 5 5 HELIX 8 8 ILE A 479 LEU A 484 1 6 HELIX 9 9 GLU A 501 SER A 505 5 5 HELIX 10 10 PRO A 523 TYR A 525 5 3 HELIX 11 11 ALA A 526 ALA A 538 1 13 HELIX 12 12 PRO A 539 VAL A 543 5 5 HELIX 13 13 ASP A 547 HIS A 550 5 4 HELIX 14 14 ASN A 557 HIS A 564 1 8 HELIX 15 15 TRP A 607 HIS A 622 1 16 HELIX 16 16 SER A 628 SER A 638 1 11 HELIX 17 17 LYS A 639 LEU A 643 5 5 HELIX 18 18 ASP A 644 LYS A 671 1 28 HELIX 19 19 ASP A 681 LEU A 685 5 5 HELIX 20 20 PRO A 686 ARG A 690 5 5 HELIX 21 21 HIS A 718 LEU A 722 5 5 HELIX 22 22 PRO A 726 TYR A 728 5 3 HELIX 23 23 THR A 737 ALA A 752 1 16 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 SSBOND 1 CYS A 708 CYS A 725 1555 1555 2.03 LINK NE2 HIS A 499 MN MN A1757 1555 1555 2.13 LINK OE2 GLU A 501 MN MN A1757 1555 1555 2.04 LINK NE2 HIS A 587 MN MN A1757 1555 1555 2.21 LINK SG CYS A 692 ZN ZN A1754 1555 1555 2.29 LINK SG CYS A 695 ZN ZN A1754 1555 1555 2.37 LINK SG CYS A 715 ZN ZN A1754 1555 1555 2.31 LINK ND1 HIS A 718 ZN ZN A1754 1555 1555 2.26 LINK MN MN A1757 O1 OGA A1770 1555 1555 2.26 LINK MN MN A1757 O2' OGA A1770 1555 1555 2.14 LINK MN MN A1757 O HOH A2054 1555 1555 2.12 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 5 GLU A 631 LYS A 635 GLU A 683 TYR A 736 SITE 2 AC2 5 HOH A2044 SITE 1 AC3 6 TRP A 486 TYR A 488 VAL A 600 ASN A 601 SITE 2 AC3 6 OGA A1770 HOH A2054 SITE 1 AC4 5 HIS A 499 GLU A 501 HIS A 587 OGA A1770 SITE 2 AC4 5 HOH A2054 SITE 1 AC5 3 HIS A 622 HIS A 718 HOH A2110 SITE 1 AC6 13 ILE A 500 TRP A 504 LEU A 541 PHE A 542 SITE 2 AC6 13 LEU A 552 VAL A 553 TYR A 586 HIS A 617 SITE 3 AC6 13 TYR A 618 ARG A 623 HOH A2051 HOH A2057 SITE 4 AC6 13 HOH A2063 SITE 1 AC7 7 ASP A 630 CYS A 699 PHE A 700 MET A 701 SITE 2 AC7 7 SER A 702 EDO A1762 HOH A2079 SITE 1 AC8 5 ARG A 666 LEU A 732 TYR A 734 THR A 737 SITE 2 AC8 5 HOH A2091 SITE 1 AC9 5 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 2 AC9 5 EDO A1760 SITE 1 BC1 2 PRO A 30 VAL A 568 SITE 1 BC2 7 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 BC2 7 VAL A 693 GLY A 711 LEU A 713 SITE 1 BC3 3 GLY A 524 ARG A 584 HOH A2120 SITE 1 BC4 5 ARG A 670 VAL A 674 ILE A 675 HOH A2090 SITE 2 BC4 5 HOH A2093 SITE 1 BC5 2 TRP A 70 SER A 457 SITE 1 BC6 7 TYR A 425 TYR A 488 SER A 494 LYS A 517 SITE 2 BC6 7 ASN A 591 OGA A1770 HOH A2047 SITE 1 BC7 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 BC7 6 GLU A 419 HOH A2020 SITE 1 BC8 14 TYR A 488 PHE A 496 HIS A 499 GLU A 501 SITE 2 BC8 14 SER A 507 ASN A 509 LYS A 517 TRP A 519 SITE 3 BC8 14 HIS A 587 ALA A 599 DMS A1756 MN A1757 SITE 4 BC8 14 EDO A1768 HOH A2054 CRYST1 142.350 142.350 152.330 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 0.007025 0.004056 0.000000 0.00000 SCALE2 0.000000 0.008112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006565 0.00000