HEADER OXIDOREDUCTASE 25-SEP-17 6EK6 TITLE CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH S49195A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B,LYSINE-SPECIFIC DEMETHYLASE COMPND 3 5B; COMPND 4 CHAIN: A; 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,CANCER/TESTIS ANTIGEN 31,CT31, COMPND 8 HISTONE DEMETHYLASE JARID1B,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN COMPND 9 1B,PLU-1,RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1,RBP2-H1; COMPND 10 EC: 1.14.11.-,1.14.11.-; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM5B, JARID1B, PLU1, RBBP2H1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS KDM5B, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,A.SZYKOWSKA,J.A.NEWMAN,G.F.RUDA,C.STRAIN-DAMERELL, AUTHOR 2 N.A.BURGESS-BROWN,S.VAZQUEZ-RODRIGUEZ,M.WRIGHT,P.E.BRENNAN, AUTHOR 3 C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,U.OPPERMANN,K.HUBER,F.VON DELFT REVDAT 2 17-JAN-24 6EK6 1 REMARK REVDAT 1 14-MAR-18 6EK6 0 JRNL AUTH V.SRIKANNATHASAN JRNL TITL CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH S49195A. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 56193 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 2875 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 56.7634 - 5.6541 1.00 2790 142 0.1873 0.2102 REMARK 3 2 5.6541 - 4.4884 1.00 2627 146 0.1420 0.1587 REMARK 3 3 4.4884 - 3.9212 1.00 2584 145 0.1357 0.1523 REMARK 3 4 3.9212 - 3.5627 1.00 2579 133 0.1554 0.1571 REMARK 3 5 3.5627 - 3.3074 1.00 2576 113 0.1828 0.2129 REMARK 3 6 3.3074 - 3.1124 1.00 2554 146 0.1894 0.2523 REMARK 3 7 3.1124 - 2.9566 1.00 2516 150 0.1858 0.2096 REMARK 3 8 2.9566 - 2.8279 1.00 2526 133 0.1918 0.2145 REMARK 3 9 2.8279 - 2.7190 1.00 2536 127 0.2024 0.2116 REMARK 3 10 2.7190 - 2.6252 1.00 2505 163 0.1888 0.2285 REMARK 3 11 2.6252 - 2.5431 1.00 2504 139 0.1925 0.1979 REMARK 3 12 2.5431 - 2.4704 1.00 2526 140 0.1868 0.2086 REMARK 3 13 2.4704 - 2.4054 1.00 2498 128 0.1926 0.2045 REMARK 3 14 2.4054 - 2.3467 1.00 2527 127 0.2058 0.2203 REMARK 3 15 2.3467 - 2.2933 1.00 2465 171 0.2089 0.2275 REMARK 3 16 2.2933 - 2.2445 1.00 2495 126 0.2102 0.2723 REMARK 3 17 2.2445 - 2.1996 1.00 2525 118 0.2336 0.2571 REMARK 3 18 2.1996 - 2.1581 1.00 2512 125 0.2434 0.2770 REMARK 3 19 2.1581 - 2.1196 1.00 2497 141 0.2512 0.2864 REMARK 3 20 2.1196 - 2.0836 1.00 2482 133 0.2614 0.2975 REMARK 3 21 2.0836 - 2.0500 1.00 2494 129 0.2700 0.2867 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.00 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 3767 REMARK 3 ANGLE : 0.867 5121 REMARK 3 CHIRALITY : 0.051 550 REMARK 3 PLANARITY : 0.006 667 REMARK 3 DIHEDRAL : 5.341 3066 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): 76.0883 66.2495 11.4468 REMARK 3 T TENSOR REMARK 3 T11: 0.1881 T22: 0.3531 REMARK 3 T33: 0.2283 T12: -0.0222 REMARK 3 T13: 0.0115 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 0.9523 L22: 0.3083 REMARK 3 L33: -0.0662 L12: 0.0233 REMARK 3 L13: -0.1244 L23: -0.0703 REMARK 3 S TENSOR REMARK 3 S11: -0.0622 S12: -0.0014 S13: 0.0216 REMARK 3 S21: -0.0220 S22: 0.0450 S23: 0.0142 REMARK 3 S31: 0.0041 S32: 0.0284 S33: -0.0000 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 6EK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-16 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 : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56258 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 64.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.30 REMARK 200 R MERGE FOR SHELL (I) : 0.12500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5A1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.8M POTTASSIUM REMARK 280 PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 100.63333 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 50.31667 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 75.47500 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 25.15833 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 125.79167 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 100.63333 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 50.31667 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 25.15833 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 75.47500 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 125.79167 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 29.0 KCAL/MOL 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 S DMS A 808 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 LYS A 432 REMARK 465 GLU A 433 REMARK 465 GLY A 443 REMARK 465 LYS A 444 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 LYS A 51 CD CE NZ REMARK 470 GLN A 71 CG CD OE1 NE2 REMARK 470 LEU A 81 CG CD1 CD2 REMARK 470 HIS A 82 ND1 CD2 CE1 NE2 REMARK 470 ARG A 375 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 404 CD OE1 OE2 REMARK 470 LYS A 408 CE NZ REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 ASP A 428 CG OD1 OD2 REMARK 470 ILE A 429 CG1 CG2 CD1 REMARK 470 LYS A 446 NZ REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 ASP A 478 CG OD1 OD2 REMARK 470 LYS A 535 CD CE NZ REMARK 470 LYS A 536 CD CE NZ REMARK 470 GLU A 540 CG CD OE1 OE2 REMARK 470 SER A 544 OG REMARK 470 LEU A 548 CG CD1 CD2 REMARK 470 LEU A 549 CG CD1 CD2 REMARK 470 GLU A 565 CG CD OE1 OE2 REMARK 470 LEU A 620 CD1 CD2 REMARK 470 ARG A 623 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 639 NZ REMARK 470 LYS A 653 CE NZ REMARK 470 GLU A 660 CD OE1 OE2 REMARK 470 LYS A 671 NZ REMARK 470 LYS A 694 NZ REMARK 470 LYS A 709 CE NZ REMARK 470 LYS A 720 CG CD CE NZ REMARK 470 GLU A 753 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 O HOH A 1093 O HOH A 1095 2.19 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 DMS A 808 C2 DMS A 808 9765 1.17 REMARK 500 C1 DMS A 808 C2 DMS A 808 9765 1.40 REMARK 500 S DMS A 808 O DMS A 808 9765 1.47 REMARK 500 O DMS A 808 C1 DMS A 808 9765 1.70 REMARK 500 S DMS A 808 C1 DMS A 808 9765 1.74 REMARK 500 C1 DMS A 808 C1 DMS A 808 9765 1.85 REMARK 500 S DMS A 808 C2 DMS A 808 9765 1.87 REMARK 500 O HOH A 906 O HOH A 987 8665 1.91 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 79.99 -107.13 REMARK 500 LEU A 93 -4.43 75.60 REMARK 500 ASP A 420 70.65 -119.45 REMARK 500 ASP A 428 140.05 -171.42 REMARK 500 PHE A 493 -4.98 76.14 REMARK 500 PHE A 700 -50.19 -150.46 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 A 802 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 91 OD1 REMARK 620 2 LEU A 413 O 150.7 REMARK 620 3 THR A 416 O 121.0 82.3 REMARK 620 4 HOH A 937 O 92.0 85.3 127.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 803 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 99.5 REMARK 620 3 90V A 804 N7 102.2 89.9 REMARK 620 4 90V A 804 O11 90.5 167.4 80.6 REMARK 620 5 HOH A 938 O 169.0 89.0 84.7 82.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 692 SG REMARK 620 2 CYS A 695 SG 108.1 REMARK 620 3 CYS A 715 SG 118.0 111.2 REMARK 620 4 HIS A 718 ND1 111.7 108.1 99.2 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 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 90V A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 813 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 814 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 815 DBREF 6EK6 A 26 99 UNP Q9UGL1 KDM5B_HUMAN 26 99 DBREF 6EK6 A 375 754 UNP Q9UGL1 KDM5B_HUMAN 375 754 SEQADV 6EK6 MET A 25 UNP Q9UGL1 INITIATING METHIONINE SEQRES 1 A 455 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 2 A 455 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS SEQRES 3 A 455 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS SEQRES 4 A 455 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 5 A 455 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG SEQRES 6 A 455 LEU ASN GLU LEU GLU ALA GLN THR ARG VAL ARG ASP TYR SEQRES 7 A 455 THR LEU ARG THR PHE GLY GLU MET ALA ASP ALA PHE LYS SEQRES 8 A 455 SER ASP TYR PHE ASN MET PRO VAL HIS MET VAL PRO THR SEQRES 9 A 455 GLU LEU VAL GLU LYS GLU PHE TRP ARG LEU VAL SER THR SEQRES 10 A 455 ILE GLU GLU ASP VAL THR VAL GLU TYR GLY ALA ASP ILE SEQRES 11 A 455 ALA SER LYS GLU PHE GLY SER GLY PHE PRO VAL ARG ASP SEQRES 12 A 455 GLY LYS ILE LYS LEU SER PRO GLU GLU GLU GLU TYR LEU SEQRES 13 A 455 ASP SER GLY TRP ASN LEU ASN ASN MET PRO VAL MET GLU SEQRES 14 A 455 GLN SER VAL LEU ALA HIS ILE THR ALA ASP ILE CYS GLY SEQRES 15 A 455 MET LYS LEU PRO TRP LEU TYR VAL GLY MET CYS PHE SER SEQRES 16 A 455 SER PHE CYS TRP HIS ILE GLU ASP HIS TRP SER TYR SER SEQRES 17 A 455 ILE ASN TYR LEU HIS TRP GLY GLU PRO LYS THR TRP TYR SEQRES 18 A 455 GLY VAL PRO GLY TYR ALA ALA GLU GLN LEU GLU ASN VAL SEQRES 19 A 455 MET LYS LYS LEU ALA PRO GLU LEU PHE VAL SER GLN PRO SEQRES 20 A 455 ASP LEU LEU HIS GLN LEU VAL THR ILE MET ASN PRO ASN SEQRES 21 A 455 THR LEU MET THR HIS GLU VAL PRO VAL TYR ARG THR ASN SEQRES 22 A 455 GLN CYS ALA GLY GLU PHE VAL ILE THR PHE PRO ARG ALA SEQRES 23 A 455 TYR HIS SER GLY PHE ASN GLN GLY PHE ASN PHE ALA GLU SEQRES 24 A 455 ALA VAL ASN PHE CYS THR VAL ASP TRP LEU PRO LEU GLY SEQRES 25 A 455 ARG GLN CYS VAL GLU HIS TYR ARG LEU LEU HIS ARG TYR SEQRES 26 A 455 CYS VAL PHE SER HIS ASP GLU MET ILE CYS LYS MET ALA SEQRES 27 A 455 SER LYS ALA ASP VAL LEU ASP VAL VAL VAL ALA SER THR SEQRES 28 A 455 VAL GLN LYS ASP MET ALA ILE MET ILE GLU ASP GLU LYS SEQRES 29 A 455 ALA LEU ARG GLU THR VAL ARG LYS LEU GLY VAL ILE ASP SEQRES 30 A 455 SER GLU ARG MET ASP PHE GLU LEU LEU PRO ASP ASP GLU SEQRES 31 A 455 ARG GLN CYS VAL LYS CYS LYS THR THR CYS PHE MET SER SEQRES 32 A 455 ALA ILE SER CYS SER CYS LYS PRO GLY LEU LEU VAL CYS SEQRES 33 A 455 LEU HIS HIS VAL LYS GLU LEU CYS SER CYS PRO PRO TYR SEQRES 34 A 455 LYS TYR LYS LEU ARG TYR ARG TYR THR LEU ASP ASP LEU SEQRES 35 A 455 TYR PRO MET MET ASN ALA LEU LYS LEU ARG ALA GLU SER HET ZN A 801 1 HET MN A 802 1 HET NI A 803 1 HET 90V A 804 21 HET DMS A 805 4 HET DMS A 806 4 HET DMS A 807 4 HET DMS A 808 4 HET EDO A 809 4 HET EDO A 810 4 HET EDO A 811 4 HET EDO A 812 4 HET EDO A 813 4 HET EDO A 814 4 HET EDO A 815 4 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM NI NICKEL (II) ION HETNAM 90V N-{(3R)-1-[3-(PROPAN-2-YL)-1H-PYRAZOLE-5- HETNAM 2 90V CARBONYL]PYRROLIDIN-3-YL}CYCLOPROPANECARBOXAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MN MN 2+ FORMUL 4 NI NI 2+ FORMUL 5 90V C15 H22 N4 O2 FORMUL 6 DMS 4(C2 H6 O S) FORMUL 10 EDO 7(C2 H6 O2) FORMUL 17 HOH *210(H2 O) HELIX 1 AA1 SER A 38 ASP A 44 1 7 HELIX 2 AA2 ASP A 44 GLU A 57 1 14 HELIX 3 AA3 LEU A 379 ASN A 395 1 17 HELIX 4 AA4 PRO A 397 VAL A 401 5 5 HELIX 5 AA5 PRO A 402 THR A 416 1 15 HELIX 6 AA6 SER A 448 TYR A 454 1 7 HELIX 7 AA7 ASN A 463 MET A 467 5 5 HELIX 8 AA8 ILE A 479 LYS A 483 5 5 HELIX 9 AA9 GLU A 501 SER A 505 5 5 HELIX 10 AB1 PRO A 523 TYR A 525 5 3 HELIX 11 AB2 ALA A 526 ALA A 538 1 13 HELIX 12 AB3 PRO A 539 PHE A 542 5 4 HELIX 13 AB4 ASP A 547 HIS A 550 5 4 HELIX 14 AB5 ASN A 557 HIS A 564 1 8 HELIX 15 AB6 ASP A 606 HIS A 622 1 17 HELIX 16 AB7 SER A 628 SER A 638 1 11 HELIX 17 AB8 LYS A 639 LEU A 643 5 5 HELIX 18 AB9 ASP A 644 LEU A 672 1 29 HELIX 19 AC1 ASP A 681 LEU A 685 5 5 HELIX 20 AC2 PRO A 686 ARG A 690 5 5 HELIX 21 AC3 HIS A 718 LEU A 722 5 5 HELIX 22 AC4 PRO A 726 TYR A 728 5 3 HELIX 23 AC5 THR A 737 SER A 754 1 18 SHEET 1 AA1 8 VAL A 34 PHE A 35 0 SHEET 2 AA1 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35 SHEET 3 AA1 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64 SHEET 4 AA1 8 TYR A 506 GLY A 514 -1 N ASN A 509 O VAL A 579 SHEET 5 AA1 8 ASN A 595 PHE A 602 -1 O GLU A 598 N TYR A 510 SHEET 6 AA1 8 TRP A 486 GLY A 490 -1 N TRP A 486 O ALA A 599 SHEET 7 AA1 8 THR A 422 ILE A 429 -1 N ASP A 428 O LEU A 487 SHEET 8 AA1 8 ARG A 86 ARG A 89 -1 N ARG A 86 O TYR A 425 SHEET 1 AA2 2 HIS A 82 PHE A 83 0 SHEET 2 AA2 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83 SHEET 1 AA3 2 GLN A 96 THR A 97 0 SHEET 2 AA3 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96 SHEET 1 AA4 4 SER A 495 HIS A 499 0 SHEET 2 AA4 4 HIS A 587 ASN A 591 -1 O GLY A 589 N PHE A 496 SHEET 3 AA4 4 LYS A 517 GLY A 521 -1 N TYR A 520 O SER A 588 SHEET 4 AA4 4 TYR A 569 GLN A 573 -1 O GLN A 573 N LYS A 517 SHEET 1 AA5 3 ASP A 676 ARG A 679 0 SHEET 2 AA5 3 TYR A 730 TYR A 734 1 O LEU A 732 N ASP A 676 SHEET 3 AA5 3 SER A 702 CYS A 706 -1 N ALA A 703 O ARG A 733 SSBOND 1 CYS A 708 CYS A 725 1555 1555 2.04 LINK OD1 ASN A 91 MN MN A 802 1555 1555 2.60 LINK O LEU A 413 MN MN A 802 1555 1555 2.70 LINK O THR A 416 MN MN A 802 1555 1555 2.64 LINK NE2 HIS A 499 NI NI A 803 1555 1555 2.18 LINK OE2 GLU A 501 NI NI A 803 1555 1555 2.11 LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.22 LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.34 LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.30 LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.07 LINK MN MN A 802 O HOH A 937 1555 1555 2.01 LINK NI NI A 803 N7 90V A 804 1555 1555 1.95 LINK NI NI A 803 O11 90V A 804 1555 1555 2.21 LINK NI NI A 803 O HOH A 938 1555 1555 2.16 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC2 6 GLU A 419 HOH A 937 SITE 1 AC3 5 HIS A 499 GLU A 501 HIS A 587 90V A 804 SITE 2 AC3 5 HOH A 938 SITE 1 AC4 14 TYR A 425 TYR A 488 SER A 495 PHE A 496 SITE 2 AC4 14 HIS A 499 GLU A 501 LYS A 517 HIS A 587 SITE 3 AC4 14 ASN A 591 ALA A 599 ASN A 601 NI A 803 SITE 4 AC4 14 HOH A 938 HOH A1035 SITE 1 AC5 7 ILE A 500 TRP A 504 HIS A 617 LEU A 621 SITE 2 AC5 7 HOH A 928 HOH A 955 HOH A1020 SITE 1 AC6 4 ARG A 666 SER A 677 THR A 737 EDO A 813 SITE 1 AC7 3 HIS A 622 HIS A 718 HOH A1041 SITE 1 AC8 4 VAL A 398 HIS A 399 HOH A 910 HOH A1066 SITE 1 AC9 8 VAL A 615 TYR A 618 ARG A 619 ARG A 623 SITE 2 AC9 8 CYS A 625 CYS A 695 LYS A 696 THR A 697 SITE 1 AD1 6 ASP A 630 CYS A 699 PHE A 700 MET A 701 SITE 2 AD1 6 SER A 702 HOH A 947 SITE 1 AD2 3 SER A 495 PHE A 496 CYS A 497 SITE 1 AD3 4 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 1 AD4 5 VAL A 674 ILE A 675 DMS A 806 HOH A 912 SITE 2 AD4 5 HOH A 917 SITE 1 AD5 1 ARG A 679 SITE 1 AD6 7 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AD6 7 VAL A 693 GLY A 711 LEU A 713 CRYST1 141.410 141.410 150.950 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 0.007072 0.004083 0.000000 0.00000 SCALE2 0.000000 0.008166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006625 0.00000