HEADER OXIDOREDUCTASE 28-JAN-16 5FUP TITLE CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH 2-OXOGLUTARATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, RESIDUES 26-101 TO 374-772; COMPND 5 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, COMPND 6 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA- COMPND 7 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1; COMPND 8 EC: 1.14.11.-; COMPND 9 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 5FUP 1 REMARK LINK REVDAT 5 24-JAN-18 5FUP 1 AUTHOR REVDAT 4 29-JUN-16 5FUP 1 JRNL REVDAT 3 01-JUN-16 5FUP 1 JRNL REVDAT 2 25-MAY-16 5FUP 1 JRNL REVDAT 1 23-MAR-16 5FUP 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. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 49907 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2412 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 71.2090 - 5.5275 1.00 3049 158 0.1903 0.2328 REMARK 3 2 5.5275 - 4.3875 1.00 2881 151 0.1414 0.1780 REMARK 3 3 4.3875 - 3.8330 1.00 2865 117 0.1451 0.1762 REMARK 3 4 3.8330 - 3.4825 1.00 2808 148 0.1622 0.1996 REMARK 3 5 3.4825 - 3.2329 1.00 2796 147 0.1809 0.2320 REMARK 3 6 3.2329 - 3.0423 1.00 2771 162 0.1956 0.2337 REMARK 3 7 3.0423 - 2.8899 1.00 2798 130 0.2042 0.2808 REMARK 3 8 2.8899 - 2.7641 1.00 2757 142 0.2166 0.2454 REMARK 3 9 2.7641 - 2.6577 1.00 2780 152 0.2097 0.2784 REMARK 3 10 2.6577 - 2.5660 1.00 2748 144 0.2052 0.2552 REMARK 3 11 2.5660 - 2.4858 1.00 2775 122 0.2022 0.2588 REMARK 3 12 2.4858 - 2.4147 1.00 2740 142 0.2084 0.2460 REMARK 3 13 2.4147 - 2.3511 1.00 2780 136 0.2093 0.2530 REMARK 3 14 2.3511 - 2.2938 1.00 2730 136 0.2077 0.2452 REMARK 3 15 2.2938 - 2.2416 1.00 2714 145 0.2291 0.2786 REMARK 3 16 2.2416 - 2.1939 1.00 2768 133 0.2396 0.3068 REMARK 3 17 2.1939 - 2.1500 1.00 2735 147 0.2428 0.2922 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.008 3873 REMARK 3 ANGLE : 1.072 5253 REMARK 3 CHIRALITY : 0.046 556 REMARK 3 PLANARITY : 0.006 677 REMARK 3 DIHEDRAL : 14.055 1435 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 5FUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1290066148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-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 : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9173 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 : 49972 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 76.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 5A1F REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 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 101.50667 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 50.75333 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 76.13000 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 25.37667 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 126.88333 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 101.50667 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 50.75333 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 25.37667 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 76.13000 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 126.88333 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 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 GLY A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 104 REMARK 465 GLY A 105 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 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 MET A 0 CG SD CE REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 ARG A 375 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 417 CG1 CG2 CD1 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 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 OD1 ASP A 428 O HOH A 2184 2.06 REMARK 500 O HOH A 2419 O HOH A 2465 2.12 REMARK 500 OE1 GLU A 452 O HOH A 2205 2.13 REMARK 500 O HOH A 2255 O HOH A 2262 2.15 REMARK 500 O LYS A 483 O HOH A 2238 2.15 REMARK 500 O GLN A 469 O HOH A 2216 2.16 REMARK 500 O HOH A 2031 O HOH A 2033 2.16 REMARK 500 O HOH A 2415 O HOH A 2464 2.17 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 MET A 0 -91.84 54.79 REMARK 500 LEU A 93 -0.03 65.70 REMARK 500 ALA A 430 103.11 -57.45 REMARK 500 GLU A 468 14.52 54.68 REMARK 500 PHE A 493 -4.47 74.87 REMARK 500 ALA A 538 67.09 -151.92 REMARK 500 ARG A 690 36.27 -140.51 REMARK 500 PHE A 700 -54.12 -151.17 REMARK 500 PHE A 700 -52.58 -151.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2297 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A2307 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A2492 DISTANCE = 7.76 ANGSTROMS 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 95.7 REMARK 620 3 HIS A 587 NE2 86.1 87.1 REMARK 620 4 AKG A1764 O5 93.1 170.5 97.3 REMARK 620 5 AKG A1764 O2 167.9 96.2 92.1 75.2 REMARK 620 6 HOH A2252 O 89.4 93.4 175.5 83.0 92.2 REMARK 620 N 1 2 3 4 5 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 692 SG REMARK 620 2 CYS A 695 SG 107.6 REMARK 620 3 CYS A 715 SG 118.9 111.8 REMARK 620 4 HIS A 718 ND1 106.2 108.2 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1756 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 706 SG REMARK 620 2 CYS A 708 SG 122.8 REMARK 620 3 CYS A 723 SG 109.7 109.9 REMARK 620 4 CYS A 725 SG 103.8 97.5 112.2 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 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1757 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1758 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2760 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2762 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2763 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2764 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2765 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2766 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2767 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2768 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2769 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 1764 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FV3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JARID1B CONSTRUCT C2 IN COMPLEX WITH N- REMARK 900 OXALYLGLYCINE. DBREF 5FUP A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5FUP A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770 SEQADV 5FUP SER A -1 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FUP MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FUP GLY A 102 UNP Q9UGL1 LINKER SEQADV 5FUP GLY A 103 UNP Q9UGL1 LINKER SEQADV 5FUP GLY A 104 UNP Q9UGL1 LINKER SEQADV 5FUP GLY A 105 UNP Q9UGL1 LINKER SEQRES 1 A 479 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 479 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 479 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 479 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 479 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 479 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 479 GLY GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE SEQRES 8 A 479 GLY GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN SEQRES 9 A 479 MET PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS SEQRES 10 A 479 GLU PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL SEQRES 11 A 479 THR VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE SEQRES 12 A 479 GLY SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SEQRES 13 A 479 SER PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN SEQRES 14 A 479 LEU ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA SEQRES 15 A 479 HIS ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP SEQRES 16 A 479 LEU TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS SEQRES 17 A 479 ILE GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS SEQRES 18 A 479 TRP GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR SEQRES 19 A 479 ALA ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA SEQRES 20 A 479 PRO GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN SEQRES 21 A 479 LEU VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS SEQRES 22 A 479 GLU VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU SEQRES 23 A 479 PHE VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE SEQRES 24 A 479 ASN GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS SEQRES 25 A 479 THR VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU SEQRES 26 A 479 HIS TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS SEQRES 27 A 479 ASP GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL SEQRES 28 A 479 LEU ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET SEQRES 29 A 479 ALA ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR SEQRES 30 A 479 VAL ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP SEQRES 31 A 479 PHE GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS SEQRES 32 A 479 CYS LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER SEQRES 33 A 479 CYS LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS SEQRES 34 A 479 GLU LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG SEQRES 35 A 479 TYR ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN SEQRES 36 A 479 ALA LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA SEQRES 37 A 479 LEU ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE HET ZN A1755 1 HET ZN A1756 1 HET MN A1757 1 HET MN A1758 1 HET EPE A1759 15 HET CL A1762 1 HET AKG A1764 10 HET EDO A2760 4 HET EDO A2762 4 HET EDO A2763 4 HET EDO A2764 4 HET EDO A2765 4 HET EDO A2766 4 HET EDO A2767 4 HET EDO A2768 4 HET EDO A2769 4 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM CL CHLORIDE ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MN 2(MN 2+) FORMUL 6 EPE C8 H18 N2 O4 S FORMUL 7 CL CL 1- FORMUL 8 AKG C5 H6 O5 FORMUL 9 EDO 9(C2 H6 O2) FORMUL 18 HOH *493(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 402 THR A 416 1 15 HELIX 5 5 SER A 448 TYR A 454 1 7 HELIX 6 6 ASN A 463 MET A 467 5 5 HELIX 7 7 SER A 470 HIS A 474 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 THR A 604 ASP A 606 5 3 HELIX 16 16 TRP A 607 LEU A 621 1 15 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 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 LINK NE2 HIS A 499 MN MN A1757 1555 1555 2.17 LINK OE2 GLU A 501 MN MN A1757 1555 1555 2.08 LINK NE2 HIS A 587 MN MN A1757 1555 1555 2.21 LINK SG CYS A 692 ZN ZN A1755 1555 1555 2.17 LINK SG CYS A 695 ZN ZN A1755 1555 1555 2.38 LINK SG CYS A 706 ZN ZN A1756 1555 1555 2.48 LINK SG CYS A 708 ZN ZN A1756 1555 1555 2.52 LINK SG CYS A 715 ZN ZN A1755 1555 1555 2.30 LINK ND1 HIS A 718 ZN ZN A1755 1555 1555 2.10 LINK SG CYS A 723 ZN ZN A1756 1555 1555 2.30 LINK SG CYS A 725 ZN ZN A1756 1555 1555 2.59 LINK MN MN A1757 O5 AKG A1764 1555 1555 2.20 LINK MN MN A1757 O2 AKG A1764 1555 1555 2.36 LINK MN MN A1757 O HOH A2252 1555 1555 2.07 LINK MN MN A1758 O HOH A2456 1555 1555 1.95 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 5 HIS A 499 GLU A 501 HIS A 587 AKG A1764 SITE 2 AC3 5 HOH A2252 SITE 1 AC4 1 HOH A2456 SITE 1 AC5 16 ILE A 500 TRP A 504 LEU A 541 LEU A 552 SITE 2 AC5 16 VAL A 553 TYR A 586 HIS A 617 TYR A 618 SITE 3 AC5 16 LEU A 621 ARG A 623 HOH A2250 HOH A2256 SITE 4 AC5 16 HOH A2289 HOH A2318 HOH A2360 HOH A2482 SITE 1 AC6 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC6 6 GLU A 419 HOH A2111 SITE 1 AC7 6 ASP A 630 CYS A 699 PHE A 700 MET A 701 SITE 2 AC7 6 SER A 702 HOH A2369 SITE 1 AC8 3 TYR A 734 HOH A2468 HOH A2485 SITE 1 AC9 6 ARG A 612 ASP A 630 MET A 658 ASP A 661 SITE 2 AC9 6 GLU A 662 HOH A2455 SITE 1 BC1 2 PRO A 30 VAL A 568 SITE 1 BC2 9 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 BC2 9 VAL A 693 GLY A 711 LEU A 712 LEU A 713 SITE 3 BC2 9 HOH A2488 SITE 1 BC3 5 GLY A 524 TYR A 525 ARG A 584 HOH A2277 SITE 2 BC3 5 HOH A2489 SITE 1 BC4 5 ARG A 670 VAL A 674 ILE A 675 HOH A2179 SITE 2 BC4 5 HOH A2397 SITE 1 BC5 4 TRP A 70 GLU A 453 SER A 457 HOH A2039 SITE 1 BC6 8 TYR A 488 GLU A 501 ALA A 599 ASN A 601 SITE 2 BC6 8 AKG A1764 HOH A2234 HOH A2252 HOH A2490 SITE 1 BC7 15 TYR A 425 TYR A 488 PHE A 496 HIS A 499 SITE 2 BC7 15 GLU A 501 SER A 507 ASN A 509 LYS A 517 SITE 3 BC7 15 TRP A 519 HIS A 587 ALA A 599 MN A1757 SITE 4 BC7 15 HOH A2252 HOH A2483 EDO A2769 CRYST1 142.340 142.340 152.260 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 0.006568 0.00000