HEADER OXIDOREDUCTASE 03-JUN-15 5A3W TITLE CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH PYRIDINE-2, TITLE 2 6-DICARBOXYLIC ACID (PDCA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, RESIDUES 26-101,374-772; 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, LYSINE-SPECIFIC DEMETHYLASE 5B EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,J.KOPEC,C.STRAIN-DAMERELL, AUTHOR 2 K.KUPINSKA,N.A.BURGESS-BROWN,F.VON DELFT,C.H.ARROWSMITH,C.BOUNTRA, AUTHOR 3 A.M.EDWARDS,U.OPPERMANN REVDAT 5 24-JAN-18 5A3W 1 AUTHOR REVDAT 4 29-JUN-16 5A3W 1 JRNL REVDAT 3 01-JUN-16 5A3W 1 JRNL REVDAT 2 25-MAY-16 5A3W 1 JRNL REVDAT 1 17-JUN-15 5A3W 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 61434 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3054 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 19.8467 - 5.5645 1.00 2906 141 0.1788 0.2314 REMARK 3 2 5.5645 - 4.4329 1.00 2773 116 0.1436 0.1706 REMARK 3 3 4.4329 - 3.8773 1.00 2710 155 0.1492 0.1618 REMARK 3 4 3.8773 - 3.5250 1.00 2683 142 0.1644 0.2067 REMARK 3 5 3.5250 - 3.2735 1.00 2681 141 0.1880 0.2040 REMARK 3 6 3.2735 - 3.0813 1.00 2665 126 0.2001 0.2330 REMARK 3 7 3.0813 - 2.9275 1.00 2664 138 0.2078 0.2271 REMARK 3 8 2.9275 - 2.8004 1.00 2649 140 0.1994 0.2489 REMARK 3 9 2.8004 - 2.6929 1.00 2647 150 0.2015 0.2192 REMARK 3 10 2.6929 - 2.6001 1.00 2633 126 0.2038 0.2401 REMARK 3 11 2.6001 - 2.5190 1.00 2629 147 0.1940 0.2100 REMARK 3 12 2.5190 - 2.4471 1.00 2636 125 0.2019 0.2625 REMARK 3 13 2.4471 - 2.3828 1.00 2628 142 0.2039 0.2543 REMARK 3 14 2.3828 - 2.3248 1.00 2635 136 0.2024 0.2127 REMARK 3 15 2.3248 - 2.2720 1.00 2607 146 0.2015 0.2234 REMARK 3 16 2.2720 - 2.2237 1.00 2600 141 0.2080 0.2300 REMARK 3 17 2.2237 - 2.1793 1.00 2618 135 0.2153 0.2674 REMARK 3 18 2.1793 - 2.1382 1.00 2603 164 0.2202 0.2522 REMARK 3 19 2.1382 - 2.1001 1.00 2608 140 0.2254 0.2448 REMARK 3 20 2.1001 - 2.0645 1.00 2604 141 0.2243 0.2801 REMARK 3 21 2.0645 - 2.0312 1.00 2622 124 0.2189 0.2715 REMARK 3 22 2.0312 - 2.0000 1.00 2579 138 0.2303 0.2468 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.50 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 3811 REMARK 3 ANGLE : 1.111 5184 REMARK 3 CHIRALITY : 0.048 552 REMARK 3 PLANARITY : 0.006 668 REMARK 3 DIHEDRAL : 14.316 1399 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 76.8468 66.0785 11.5314 REMARK 3 T TENSOR REMARK 3 T11: 0.0020 T22: 0.3566 REMARK 3 T33: 0.1365 T12: -0.0537 REMARK 3 T13: 0.0078 T23: -0.0645 REMARK 3 L TENSOR REMARK 3 L11: 0.0828 L22: 0.0854 REMARK 3 L33: 0.0150 L12: 0.0334 REMARK 3 L13: -0.0059 L23: -0.0516 REMARK 3 S TENSOR REMARK 3 S11: -0.0317 S12: -0.0338 S13: 0.0935 REMARK 3 S21: -0.0556 S22: -0.0044 S23: 0.0441 REMARK 3 S31: 0.0029 S32: 0.0749 S33: -0.0191 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 5A3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1290063957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 0.976250 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : MIRRORS 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 : 61492 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.90 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.80 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4-AUTOMR REMARK 200 STARTING MODEL: PDB ENTRY 51AF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 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 101.50400 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 50.75200 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 76.12800 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 25.37600 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 126.88000 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 101.50400 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 50.75200 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 25.37600 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 76.12800 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 126.88000 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 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 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 465 ASN A 771 REMARK 465 LYS A 772 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 LEU A 81 CG CD1 CD2 REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 99 CG1 CG2 REMARK 470 LYS A 100 O CG CD CE NZ 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 ASP A 442 CG OD1 OD2 REMARK 470 ILE A 445 CG1 CG2 CD1 REMARK 470 LYS A 446 NZ REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 GLN A 545 CG CD OE1 NE2 REMARK 470 LEU A 549 CG CD1 CD2 REMARK 470 LYS A 653 CE NZ REMARK 470 LYS A 720 CG CD CE NZ REMARK 470 LYS A 749 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 2143 O HOH A 2178 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 78.08 -110.12 REMARK 500 LEU A 93 -5.42 70.54 REMARK 500 ILE A 479 47.36 32.81 REMARK 500 PHE A 493 -5.41 76.43 REMARK 500 PHE A 700 -52.32 -150.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE): REMARK 600 HEPES REMARK 600 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (LIG): REMARK 600 PYRIDINE-2,6-DICARBOXYLIC ACID -PDCA 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 ZN A1754 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 692 SG REMARK 620 2 CYS A 695 SG 108.4 REMARK 620 3 HIS A 718 ND1 107.8 108.7 REMARK 620 4 CYS A 715 SG 116.8 112.2 102.5 REMARK 620 N 1 2 3 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 725 SG REMARK 620 2 CYS A 706 SG 104.9 REMARK 620 3 CYS A 708 SG 102.9 121.5 REMARK 620 4 CYS A 723 SG 112.5 110.4 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1756 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 419 O REMARK 620 2 HOH A2051 O 125.0 REMARK 620 3 HOH A2049 O 63.7 149.4 REMARK 620 4 LEU A 413 O 113.5 111.3 85.8 REMARK 620 5 THR A 416 O 71.5 79.8 127.6 88.2 REMARK 620 6 ASN A 91 OD1 92.7 69.9 80.9 141.4 128.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1758 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PD2 A1757 O21 REMARK 620 2 PD2 A1757 N1 79.4 REMARK 620 3 HOH A2109 O 92.7 81.9 REMARK 620 4 HIS A 587 NE2 172.6 101.7 94.7 REMARK 620 5 HIS A 499 NE2 86.7 100.2 177.6 85.9 REMARK 620 6 GLU A 501 OE2 95.8 166.1 85.3 84.8 92.5 REMARK 620 N 1 2 3 4 5 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 ZN A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PD2 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 PO4 A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A3N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDOAM25A REMARK 900 RELATED ID: 5A3T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDM5-C49 REMARK 900 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)( ETHYL)AMINO)-2-OXOETHYL)AMINO) REMARK 900 METHYL) ISONICOTINIC ACID ). REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE REMARK 999 L101 TO G369 WAS DELETED AND LINKED BY FOUR GLYCINE REMARK 999 RESIDUES (GLYCINE LINKER). DBREF 5A3W A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5A3W A 374 772 UNP Q9UGL1 KDM5B_HUMAN 374 772 SEQADV 5A3W SER A -1 UNP Q9UGL1 EXPRESSION TAG SEQADV 5A3W MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQADV 5A3W GLY A 102 UNP Q9UGL1 LINKER SEQADV 5A3W GLY A 103 UNP Q9UGL1 LINKER SEQADV 5A3W GLY A 104 UNP Q9UGL1 LINKER SEQADV 5A3W GLY A 105 UNP Q9UGL1 LINKER SEQRES 1 A 481 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 481 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 481 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 481 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 481 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 481 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 481 GLY GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE SEQRES 8 A 481 GLY GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN SEQRES 9 A 481 MET PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS SEQRES 10 A 481 GLU PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL SEQRES 11 A 481 THR VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE SEQRES 12 A 481 GLY SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SEQRES 13 A 481 SER PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN SEQRES 14 A 481 LEU ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA SEQRES 15 A 481 HIS ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP SEQRES 16 A 481 LEU TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS SEQRES 17 A 481 ILE GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS SEQRES 18 A 481 TRP GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR SEQRES 19 A 481 ALA ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA SEQRES 20 A 481 PRO GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN SEQRES 21 A 481 LEU VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS SEQRES 22 A 481 GLU VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU SEQRES 23 A 481 PHE VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE SEQRES 24 A 481 ASN GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS SEQRES 25 A 481 THR VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU SEQRES 26 A 481 HIS TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS SEQRES 27 A 481 ASP GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL SEQRES 28 A 481 LEU ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET SEQRES 29 A 481 ALA ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR SEQRES 30 A 481 VAL ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP SEQRES 31 A 481 PHE GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS SEQRES 32 A 481 CYS LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER SEQRES 33 A 481 CYS LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS SEQRES 34 A 481 GLU LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG SEQRES 35 A 481 TYR ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN SEQRES 36 A 481 ALA LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA SEQRES 37 A 481 LEU ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE ASN LYS HET ZN A1754 1 HET ZN A1755 1 HET NA A1756 1 HET PD2 A1757 12 HET MN A1758 1 HET PO4 A1759 5 HET EPE A1760 15 HET EDO A1761 4 HET EDO A1762 4 HET EDO A1763 4 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM PD2 PYRIDINE-2,4-DICARBOXYLIC ACID HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 NA NA 1+ FORMUL 5 PD2 C7 H5 N O4 FORMUL 6 MN MN 2+ FORMUL 7 PO4 O4 P 3- FORMUL 8 EPE C8 H18 N2 O4 S FORMUL 9 EDO 3(C2 H6 O2) FORMUL 12 HOH *229(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 448 TYR A 454 1 7 HELIX 7 7 ASN A 462 MET A 467 1 6 HELIX 8 8 SER A 470 ILE A 475 5 6 HELIX 9 9 ILE A 479 LYS A 483 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 ASP A 547 HIS A 550 5 4 HELIX 15 15 ASN A 557 HIS A 564 1 8 HELIX 16 16 TRP A 607 HIS A 622 1 16 HELIX 17 17 SER A 628 LYS A 639 1 12 HELIX 18 18 ALA A 640 LEU A 643 5 4 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 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 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 ZN ZN A1754 SG CYS A 692 1555 1555 2.28 LINK ZN ZN A1754 SG CYS A 695 1555 1555 2.33 LINK ZN ZN A1754 ND1 HIS A 718 1555 1555 2.10 LINK ZN ZN A1754 SG CYS A 715 1555 1555 2.26 LINK ZN ZN A1755 SG CYS A 725 1555 1555 2.52 LINK ZN ZN A1755 SG CYS A 706 1555 1555 2.37 LINK ZN ZN A1755 SG CYS A 708 1555 1555 2.64 LINK ZN ZN A1755 SG CYS A 723 1555 1555 2.32 LINK NA NA A1756 O GLU A 419 1555 1555 2.87 LINK NA NA A1756 O HOH A2051 1555 1555 3.19 LINK NA NA A1756 O HOH A2049 1555 1555 2.23 LINK NA NA A1756 O LEU A 413 1555 1555 2.72 LINK NA NA A1756 O THR A 416 1555 1555 2.49 LINK NA NA A1756 OD1 ASN A 91 1555 1555 2.84 LINK O21 PD2 A1757 MN MN A1758 1555 1555 2.12 LINK N1 PD2 A1757 MN MN A1758 1555 1555 2.11 LINK MN MN A1758 O HOH A2109 1555 1555 2.21 LINK MN MN A1758 NE2 HIS A 587 1555 1555 2.30 LINK MN MN A1758 NE2 HIS A 499 1555 1555 2.16 LINK MN MN A1758 OE2 GLU A 501 1555 1555 2.07 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 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC3 6 GLU A 419 HOH A2049 SITE 1 AC4 15 ARG A 98 TYR A 425 TYR A 488 PHE A 496 SITE 2 AC4 15 HIS A 499 GLU A 501 LYS A 517 TRP A 519 SITE 3 AC4 15 HIS A 587 MN A1758 HOH A2098 HOH A2108 SITE 4 AC4 15 HOH A2109 HOH A2113 HOH A2228 SITE 1 AC5 5 HIS A 499 GLU A 501 HIS A 587 PD2 A1757 SITE 2 AC5 5 HOH A2109 SITE 1 AC6 4 HIS A 622 LYS A 694 HIS A 718 HOH A2150 SITE 1 AC7 18 ILE A 500 TRP A 504 GLU A 531 MET A 534 SITE 2 AC7 18 LEU A 541 PHE A 542 LEU A 552 VAL A 553 SITE 3 AC7 18 TYR A 586 HIS A 617 TYR A 618 LEU A 621 SITE 4 AC7 18 ARG A 623 HOH A2102 HOH A2107 HOH A2129 SITE 5 AC7 18 HOH A2155 HOH A2229 SITE 1 AC8 8 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AC8 8 VAL A 693 GLY A 711 LEU A 712 LEU A 713 SITE 1 AC9 5 VAL A 674 ILE A 675 LEU A 732 HOH A2186 SITE 2 AC9 5 HOH A2190 SITE 1 BC1 8 ALA A 386 ASP A 387 LYS A 390 MET A 491 SITE 2 BC1 8 CYS A 492 GLU A 515 GLY A 593 PHE A 594 CRYST1 142.102 142.102 152.256 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 0.007037 0.004063 0.000000 0.00000 SCALE2 0.000000 0.008126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006568 0.00000