HEADER OXIDOREDUCTASE 04-MAR-16 5FY4 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX TITLE 2 WITH SUCCINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, RESIDUES, 26-101 AND 374-770; 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, LYSINE-SPECIFIC DEMETHYLASE 5B, COMPND 8 LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 9 EC: 1.14.11.-; COMPND 10 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_VECTOR: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, JARID1B, PLU1, TCA INTERMEDIATE EXPDTA X-RAY DIFFRACTION AUTHOR R.NOWAK,V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,K.KUPINSKA,C.STRAIN- AUTHOR 2 DAMERELL,A.SZYKOWSKA,F.VON DELFT,N.A.BURGESS-BROWN,C.H.ARROWSMITH, AUTHOR 3 C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN REVDAT 4 10-JAN-24 5FY4 1 REMARK REVDAT 3 15-NOV-23 5FY4 1 REMARK ATOM REVDAT 2 24-JAN-18 5FY4 1 AUTHOR JRNL REVDAT 1 22-MAR-17 5FY4 0 JRNL AUTH R.NOWAK,V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,K.KUPINSKA, JRNL AUTH 2 C.STRAIN-DAMERELL,A.SZYKOWSKA,F.VON DELFT,N.A.BURGESS-BROWN, JRNL AUTH 3 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B JRNL TITL 2 IN COMPLEX WITH SUCCINATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 53299 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2660 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 71.1107 - 5.6028 1.00 2951 123 0.1799 0.1999 REMARK 3 2 5.6028 - 4.4473 1.00 2740 153 0.1430 0.1737 REMARK 3 3 4.4473 - 3.8852 1.00 2738 131 0.1474 0.1613 REMARK 3 4 3.8852 - 3.5300 1.00 2680 140 0.1713 0.2055 REMARK 3 5 3.5300 - 3.2770 1.00 2708 127 0.1933 0.2322 REMARK 3 6 3.2770 - 3.0838 1.00 2643 147 0.2120 0.2669 REMARK 3 7 3.0838 - 2.9293 1.00 2647 157 0.2168 0.2651 REMARK 3 8 2.9293 - 2.8018 1.00 2636 150 0.2196 0.2604 REMARK 3 9 2.8018 - 2.6939 1.00 2668 136 0.2247 0.2874 REMARK 3 10 2.6939 - 2.6010 1.00 2593 160 0.2236 0.2428 REMARK 3 11 2.6010 - 2.5196 1.00 2649 139 0.2203 0.2434 REMARK 3 12 2.5196 - 2.4476 1.00 2624 140 0.2358 0.3078 REMARK 3 13 2.4476 - 2.3832 1.00 2635 137 0.2428 0.2966 REMARK 3 14 2.3832 - 2.3250 1.00 2639 134 0.2425 0.2611 REMARK 3 15 2.3250 - 2.2722 1.00 2623 134 0.2541 0.3012 REMARK 3 16 2.2722 - 2.2238 1.00 2582 155 0.2694 0.3137 REMARK 3 17 2.2238 - 2.1793 1.00 2615 143 0.2938 0.3215 REMARK 3 18 2.1793 - 2.1382 1.00 2638 130 0.3044 0.3320 REMARK 3 19 2.1382 - 2.1000 1.00 2630 124 0.3268 0.4153 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 2.00 REMARK 3 SHRINKAGE RADIUS : 2.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: GLYCINE LINKER DOES NOT EXIST IN REMARK 3 COORDINATES. REMARK 4 REMARK 4 5FY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-15 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 : 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) : 0.91732 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 95.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.50 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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 5A3P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0, 0.5M POTASSIUM REMARK 280 PHOSPHATE DIBASIC, 0.5M 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 101.40000 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 50.70000 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 76.05000 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 25.35000 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 126.75000 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 101.40000 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 50.70000 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 25.35000 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 76.05000 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 126.75000 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 MN MN A1764 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2209 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 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 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 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 PHE A 434 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 445 CB CG1 CG2 CD1 REMARK 470 ASP A 547 CG OD1 OD2 REMARK 470 LEU A 549 CG CD1 CD2 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 NE2 GLN A 545 O HIS A 550 2.09 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 2178 O HOH A 2229 10665 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 LEU A 93 -6.12 69.18 REMARK 500 ASP A 428 35.74 39.09 REMARK 500 PHE A 493 -5.90 74.47 REMARK 500 ASP A 547 165.26 62.13 REMARK 500 GLN A 551 135.63 -36.04 REMARK 500 PHE A 700 -52.27 -148.17 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1757 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1758 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1760 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1761 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1763 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1764 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1765 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FUM A 1767 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH N05859B REMARK 900 RELATED ID: 5FXW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH OXALOACETATE REMARK 900 RELATED ID: 5FXZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH CITRATE REMARK 900 RELATED ID: 5FY0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH L-MALATE REMARK 900 RELATED ID: 5FY1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH N08619B REMARK 900 RELATED ID: 5FY5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FY7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FY8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO- REMARK 900 ISOCITRATE REMARK 900 RELATED ID: 5FY9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 5FYB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC1648 REMARK 900 RELATED ID: 5FYC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FYH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FYI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 5FYM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH D-2-HYDROXYGLUTARATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES REMARK 999 102-373 WERE DELETED FROM THE ORIGINAL SEQUENCE Q9UGL1. REMARK 999 DELETED RESIDUES WERE LINKED WITH 4 GLYCINE LINKER (GGGG). DBREF 5FY4 A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5FY4 A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770 SEQADV 5FY4 SER A 24 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FY4 MET A 25 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FY4 GLY A 102 UNP Q9UGL1 LINKER SEQADV 5FY4 GLY A 103 UNP Q9UGL1 LINKER SEQADV 5FY4 GLY A 104 UNP Q9UGL1 LINKER SEQADV 5FY4 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 A1754 1 HET MN A1755 1 HET MN A1756 1 HET EDO A1757 4 HET EDO A1758 4 HET EDO A1759 4 HET EDO A1760 4 HET EDO A1761 4 HET EDO A1762 4 HET EDO A1763 4 HET MN A1764 1 HET MN A1765 1 HET MN A1766 1 HET FUM A1767 8 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM FUM FUMARIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MN 5(MN 2+) FORMUL 5 EDO 7(C2 H6 O2) FORMUL 15 FUM C4 H4 O4 FORMUL 16 HOH *237(H2 O) HELIX 1 1 SER A 38 ALA A 43 1 6 HELIX 2 2 ASP A 44 GLU A 57 1 14 HELIX 3 3 LEU A 379 ASN A 395 1 17 HELIX 4 4 PRO A 397 VAL A 401 5 5 HELIX 5 5 PRO A 402 THR A 416 1 15 HELIX 6 6 SER A 431 GLY A 435 1 5 HELIX 7 7 SER A 448 TYR A 454 1 7 HELIX 8 8 ASN A 463 MET A 467 5 5 HELIX 9 9 VAL A 471 ILE A 475 5 5 HELIX 10 10 GLU A 501 SER A 505 5 5 HELIX 11 11 PRO A 523 TYR A 525 5 3 HELIX 12 12 ALA A 526 ALA A 538 1 13 HELIX 13 13 PRO A 539 VAL A 543 5 5 HELIX 14 14 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 HIS A 622 1 16 HELIX 17 17 SER A 628 SER A 638 1 11 HELIX 18 18 LYS A 639 LEU A 643 5 5 HELIX 19 19 ASP A 644 LYS A 671 1 28 HELIX 20 20 ASP A 681 LEU A 685 5 5 HELIX 21 21 PRO A 686 ARG A 690 5 5 HELIX 22 22 HIS A 718 LEU A 722 5 5 HELIX 23 23 PRO A 726 TYR A 728 5 3 HELIX 24 24 THR A 737 GLU A 753 1 17 SHEET 1 AA 8 VAL A 34 PHE A 35 0 SHEET 2 AA 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35 SHEET 3 AA 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64 SHEET 4 AA 8 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581 SHEET 5 AA 8 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512 SHEET 6 AA 8 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599 SHEET 7 AA 8 THR A 422 ALA A 430 -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 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 6 LEU A 90 LEU A 413 THR A 416 GLU A 419 SITE 2 AC2 6 HOH A2038 HOH A2040 SITE 1 AC3 5 SER A 677 LEU A 732 THR A 737 EDO A1762 SITE 2 AC3 5 HOH A2194 SITE 1 AC4 5 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 2 AC4 5 HOH A2161 SITE 1 AC5 3 PRO A 30 PRO A 567 VAL A 568 SITE 1 AC6 8 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AC6 8 VAL A 693 GLY A 711 LEU A 712 LEU A 713 SITE 1 AC7 3 GLY A 524 TYR A 525 ARG A 584 SITE 1 AC8 6 ARG A 670 VAL A 674 ILE A 675 EDO A1757 SITE 2 AC8 6 HOH A2081 HOH A2193 SITE 1 AC9 1 HIS A 564 SITE 1 BC1 2 VAL A 398 HIS A 399 SITE 1 BC2 6 HIS A 499 GLU A 501 HIS A 587 FUM A1767 SITE 2 BC2 6 HOH A2047 HOH A2107 SITE 1 BC3 13 TYR A 425 TYR A 488 PHE A 496 HIS A 499 SITE 2 BC3 13 ASN A 509 LYS A 517 TRP A 519 HIS A 587 SITE 3 BC3 13 MN A1765 HOH A2045 HOH A2047 HOH A2107 SITE 4 BC3 13 HOH A2237 CRYST1 142.140 142.140 152.100 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 0.007035 0.004062 0.000000 0.00000 SCALE2 0.000000 0.008124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006575 0.00000