HEADER OXIDOREDUCTASE 19-SEP-17 6EIU TITLE CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ29A 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_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS KDM5B LYSINE SPECIFIC DEMETHYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,J.A.NEWMAN,A.SZYKOWSKA,M.WRIGHT,G.F.RUDA, AUTHOR 2 S.A.VAZQUEZ-RODRIGUEZ,K.KUPINSKA,C.STRAIN-DAMERELL,N.A.BURGESS- AUTHOR 3 BROWN,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,U.OPPERMANN,K.HUBER,F.VON AUTHOR 4 DELFT REVDAT 1 02-MAY-18 6EIU 0 JRNL AUTH V.SRIKANNATHASAN JRNL TITL CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ29A. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 82204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 4063 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 65.4256 - 5.6213 1.00 2973 154 0.1967 0.2177 REMARK 3 2 5.6213 - 4.4621 1.00 2830 124 0.1531 0.1664 REMARK 3 3 4.4621 - 3.8981 1.00 2774 132 0.1572 0.1920 REMARK 3 4 3.8981 - 3.5417 1.00 2772 123 0.1750 0.1879 REMARK 3 5 3.5417 - 3.2879 1.00 2720 134 0.1933 0.2023 REMARK 3 6 3.2879 - 3.0940 1.00 2724 138 0.2047 0.2136 REMARK 3 7 3.0940 - 2.9391 1.00 2734 131 0.2062 0.2468 REMARK 3 8 2.9391 - 2.8112 1.00 2686 136 0.2028 0.2603 REMARK 3 9 2.8112 - 2.7029 1.00 2682 159 0.2043 0.2150 REMARK 3 10 2.7029 - 2.6097 1.00 2685 134 0.2082 0.2019 REMARK 3 11 2.6097 - 2.5281 1.00 2689 157 0.1994 0.2376 REMARK 3 12 2.5281 - 2.4558 1.00 2690 133 0.2015 0.2359 REMARK 3 13 2.4558 - 2.3911 1.00 2647 139 0.2040 0.2470 REMARK 3 14 2.3911 - 2.3328 1.00 2688 153 0.2104 0.2271 REMARK 3 15 2.3328 - 2.2798 1.00 2672 131 0.2060 0.2619 REMARK 3 16 2.2798 - 2.2312 1.00 2670 136 0.2204 0.2462 REMARK 3 17 2.2312 - 2.1866 1.00 2663 157 0.2229 0.2234 REMARK 3 18 2.1866 - 2.1453 1.00 2659 131 0.2213 0.2489 REMARK 3 19 2.1453 - 2.1070 1.00 2661 136 0.2130 0.2655 REMARK 3 20 2.1070 - 2.0713 1.00 2694 128 0.2200 0.2184 REMARK 3 21 2.0713 - 2.0379 1.00 2632 153 0.2185 0.2457 REMARK 3 22 2.0379 - 2.0065 1.00 2651 156 0.2312 0.2707 REMARK 3 23 2.0065 - 1.9770 1.00 2633 161 0.2479 0.2930 REMARK 3 24 1.9770 - 1.9492 1.00 2636 145 0.2672 0.2952 REMARK 3 25 1.9492 - 1.9228 1.00 2652 143 0.2632 0.2743 REMARK 3 26 1.9228 - 1.8979 1.00 2639 149 0.2696 0.2784 REMARK 3 27 1.8979 - 1.8741 1.00 2653 153 0.2806 0.2825 REMARK 3 28 1.8741 - 1.8516 1.00 2659 117 0.2930 0.3633 REMARK 3 29 1.8516 - 1.8300 1.00 2673 120 0.3060 0.3231 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.33 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 3782 REMARK 3 ANGLE : 0.866 5144 REMARK 3 CHIRALITY : 0.056 553 REMARK 3 PLANARITY : 0.006 682 REMARK 3 DIHEDRAL : 4.405 3064 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): 77.2703 66.7046 11.6379 REMARK 3 T TENSOR REMARK 3 T11: 0.2296 T22: 0.3838 REMARK 3 T33: 0.2852 T12: -0.0157 REMARK 3 T13: 0.0257 T23: -0.0314 REMARK 3 L TENSOR REMARK 3 L11: 1.4791 L22: 0.3328 REMARK 3 L33: 0.2194 L12: 0.1879 REMARK 3 L13: 0.2675 L23: -0.0568 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: 0.0451 S13: 0.0890 REMARK 3 S21: -0.0122 S22: 0.0225 S23: 0.0312 REMARK 3 S31: -0.0036 S32: 0.0687 S33: -0.0009 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 6EIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-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 : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 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 : 82282 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 124.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.80 REMARK 200 R MERGE FOR SHELL (I) : 2.85800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.28 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 102.54667 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 51.27333 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 76.91000 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 25.63667 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 128.18333 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 102.54667 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 51.27333 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 25.63667 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 76.91000 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 128.18333 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 TOTAL BURIED SURFACE AREA: 3130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 26.0 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 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 369 REMARK 465 GLY A 370 REMARK 465 GLY A 371 REMARK 465 GLY A 372 REMARK 465 GLY A 373 REMARK 465 ASP A 442 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 PHE A 74 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 HIS A 399 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 408 CE NZ REMARK 470 ILE A 417 CG1 CG2 CD1 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 ASP A 420 CG OD1 OD2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 LYS A 446 NZ REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 GLU A 453 CG CD OE1 OE2 REMARK 470 GLU A 468 CG CD OE1 OE2 REMARK 470 ASP A 478 CG OD1 OD2 REMARK 470 LYS A 483 CD CE NZ 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 GLN A 545 CG CD OE1 NE2 REMARK 470 ASP A 547 CG OD1 OD2 REMARK 470 LEU A 548 CG CD1 CD2 REMARK 470 LEU A 549 CG CD1 CD2 REMARK 470 HIS A 550 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 551 CG CD OE1 NE2 REMARK 470 GLU A 565 CG CD OE1 OE2 REMARK 470 LEU A 620 CD1 CD2 REMARK 470 LYS A 639 NZ REMARK 470 LYS A 653 CE NZ 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 OG SER A 470 O HOH A 901 1.82 REMARK 500 NH1 ARG A 98 O HOH A 902 1.89 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 1126 O HOH A 1146 10665 2.07 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 75.85 -118.14 REMARK 500 ARG A 375 -151.53 -124.20 REMARK 500 PHE A 434 99.21 -162.42 REMARK 500 LEU A 472 -9.05 -54.91 REMARK 500 PHE A 493 -6.70 81.95 REMARK 500 PHE A 700 -51.50 -150.82 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 LEU A 90 O REMARK 620 2 ASN A 91 OD1 78.0 REMARK 620 3 HOH A 903 O 132.7 70.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 803 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 100.0 REMARK 620 3 HIS A 587 NE2 86.2 86.1 REMARK 620 4 B6T A 804 N1 91.2 167.3 100.6 REMARK 620 5 HOH A1044 O 91.2 88.9 173.8 85.0 REMARK 620 6 HOH A 934 O 178.2 80.7 92.1 88.3 90.5 REMARK 620 N 1 2 3 4 5 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 106.6 REMARK 620 3 CYS A 715 SG 117.6 112.4 REMARK 620 4 HIS A 718 ND1 110.9 109.5 99.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 817 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 706 SG REMARK 620 2 CYS A 708 SG 122.2 REMARK 620 3 CYS A 723 SG 104.2 105.5 REMARK 620 4 CYS A 725 SG 112.4 97.5 115.5 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 MN A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B6T 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 DMS A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 816 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 817 DBREF 6EIU A 26 100 UNP Q9UGL1 KDM5B_HUMAN 26 100 DBREF 6EIU A 374 754 UNP Q9UGL1 KDM5B_HUMAN 374 754 SEQADV 6EIU MET A 25 UNP Q9UGL1 INITIATING METHIONINE SEQADV 6EIU LEU A 369 UNP Q9UGL1 LINKER SEQADV 6EIU GLY A 370 UNP Q9UGL1 LINKER SEQADV 6EIU GLY A 371 UNP Q9UGL1 LINKER SEQADV 6EIU GLY A 372 UNP Q9UGL1 LINKER SEQADV 6EIU GLY A 373 UNP Q9UGL1 LINKER SEQRES 1 A 462 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 2 A 462 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS SEQRES 3 A 462 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS SEQRES 4 A 462 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 5 A 462 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG SEQRES 6 A 462 LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU GLY SEQRES 7 A 462 GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE GLY SEQRES 8 A 462 GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN MET SEQRES 9 A 462 PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS GLU SEQRES 10 A 462 PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL THR SEQRES 11 A 462 VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE GLY SEQRES 12 A 462 SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SER SEQRES 13 A 462 PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN LEU SEQRES 14 A 462 ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA HIS SEQRES 15 A 462 ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP LEU SEQRES 16 A 462 TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS ILE SEQRES 17 A 462 GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS TRP SEQRES 18 A 462 GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR ALA SEQRES 19 A 462 ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA PRO SEQRES 20 A 462 GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN LEU SEQRES 21 A 462 VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS GLU SEQRES 22 A 462 VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU PHE SEQRES 23 A 462 VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE ASN SEQRES 24 A 462 GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS THR SEQRES 25 A 462 VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS SEQRES 26 A 462 TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS ASP SEQRES 27 A 462 GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL LEU SEQRES 28 A 462 ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET ALA SEQRES 29 A 462 ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR VAL SEQRES 30 A 462 ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP PHE SEQRES 31 A 462 GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS SEQRES 32 A 462 LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER CYS SEQRES 33 A 462 LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU SEQRES 34 A 462 LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR SEQRES 35 A 462 ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN ALA SEQRES 36 A 462 LEU LYS LEU ARG ALA GLU SER HET ZN A 801 1 HET MN A 802 1 HET MN A 803 1 HET B6T A 804 21 HET DMS A 805 4 HET DMS A 806 4 HET DMS A 807 4 HET DMS A 808 4 HET DMS A 809 4 HET DMS A 810 4 HET DMS A 811 4 HET EDO A 812 4 HET EDO A 813 4 HET EDO A 814 4 HET EDO A 815 4 HET EDO A 816 4 HET ZN A 817 1 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM B6T 8-OXIDANYL-6-PHENYL-7-PROPAN-2-YL-IMIDAZO[1,2- HETNAM 2 B6T B]PYRIDAZINE-3-CARBONITRILE HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 3 MN 2(MN 2+) FORMUL 5 B6T C16 H14 N4 O FORMUL 6 DMS 7(C2 H6 O S) FORMUL 13 EDO 5(C2 H6 O2) FORMUL 19 HOH *280(H2 O) HELIX 1 AA1 SER A 38 ALA A 43 1 6 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 VAL A 471 ILE A 475 5 5 HELIX 9 AA9 ILE A 479 LEU A 484 1 6 HELIX 10 AB1 GLU A 501 SER A 505 5 5 HELIX 11 AB2 PRO A 523 TYR A 525 5 3 HELIX 12 AB3 ALA A 526 ALA A 538 1 13 HELIX 13 AB4 PRO A 539 VAL A 543 5 5 HELIX 14 AB5 ASN A 557 HIS A 564 1 8 HELIX 15 AB6 THR A 604 ASP A 606 5 3 HELIX 16 AB7 TRP A 607 HIS A 622 1 16 HELIX 17 AB8 SER A 628 LYS A 639 1 12 HELIX 18 AB9 ALA A 640 LEU A 643 5 4 HELIX 19 AC1 ASP A 644 LEU A 672 1 29 HELIX 20 AC2 ASP A 681 LEU A 685 5 5 HELIX 21 AC3 PRO A 686 ARG A 690 5 5 HELIX 22 AC4 HIS A 718 LEU A 722 5 5 HELIX 23 AC5 PRO A 726 TYR A 728 5 3 HELIX 24 AC6 THR A 737 GLU A 753 1 17 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 SER A 507 O THR A 581 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 HIS A 587 N HIS A 499 SHEET 3 AA4 4 LYS A 517 GLY A 521 -1 N THR A 518 O PHE A 590 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 LINK O LEU A 90 MN MN A 802 1555 1555 2.66 LINK OD1 ASN A 91 MN MN A 802 1555 1555 2.62 LINK NE2 HIS A 499 MN MN A 803 1555 1555 2.12 LINK OE2 GLU A 501 MN MN A 803 1555 1555 2.11 LINK NE2 HIS A 587 MN MN A 803 1555 1555 2.19 LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.30 LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.39 LINK SG CYS A 706 ZN ZN A 817 1555 1555 2.52 LINK SG BCYS A 708 ZN ZN A 817 1555 1555 2.19 LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.36 LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.11 LINK SG CYS A 723 ZN ZN A 817 1555 1555 2.30 LINK SG CYS A 725 ZN ZN A 817 1555 1555 2.71 LINK MN MN A 802 O HOH A 903 1555 1555 2.09 LINK MN MN A 803 N1 B6T A 804 1555 1555 2.08 LINK MN MN A 803 O HOH A1044 1555 1555 2.17 LINK MN MN A 803 O HOH A 934 1555 1555 2.17 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 5 LEU A 90 ASN A 91 LEU A 413 GLU A 419 SITE 2 AC2 5 HOH A 903 SITE 1 AC3 6 HIS A 499 GLU A 501 HIS A 587 B6T A 804 SITE 2 AC3 6 HOH A 934 HOH A1044 SITE 1 AC4 16 ARG A 98 TYR A 425 ALA A 427 TYR A 488 SITE 2 AC4 16 PHE A 496 HIS A 499 ASN A 509 LYS A 517 SITE 3 AC4 16 HIS A 587 ASN A 591 MN A 803 DMS A 805 SITE 4 AC4 16 HOH A 902 HOH A 934 HOH A1044 HOH A1106 SITE 1 AC5 9 GLN A 88 GLN A 96 THR A 97 TYR A 425 SITE 2 AC5 9 SER A 495 PHE A 496 CYS A 497 B6T A 804 SITE 3 AC5 9 HOH A 988 SITE 1 AC6 5 ARG A 98 VAL A 99 TRP A 486 TYR A 488 SITE 2 AC6 5 DMS A 807 SITE 1 AC7 8 TRP A 486 TYR A 488 SER A 507 ALA A 599 SITE 2 AC7 8 VAL A 600 ASN A 601 DMS A 806 HOH A1044 SITE 1 AC8 6 TRP A 504 ARG A 584 HIS A 617 TYR A 618 SITE 2 AC8 6 LEU A 621 ARG A 623 SITE 1 AC9 3 HIS A 622 HIS A 718 HOH A1041 SITE 1 AD1 4 GLU A 631 LYS A 635 GLU A 683 TYR A 736 SITE 1 AD2 5 ARG A 666 SER A 677 LEU A 732 THR A 737 SITE 2 AD2 5 HOH A1029 SITE 1 AD3 6 PHE A 83 GLY A 426 ALA A 427 ASP A 428 SITE 2 AD3 6 LEU A 487 VAL A 489 SITE 1 AD4 8 VAL A 615 TYR A 618 ARG A 619 ARG A 623 SITE 2 AD4 8 CYS A 625 CYS A 695 LYS A 696 THR A 697 SITE 1 AD5 5 ARG A 670 VAL A 674 ILE A 675 HOH A 910 SITE 2 AD5 5 HOH A 957 SITE 1 AD6 4 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 1 AD7 7 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AD7 7 VAL A 693 GLY A 711 LEU A 713 SITE 1 AD8 4 CYS A 706 CYS A 708 CYS A 723 CYS A 725 CRYST1 143.380 143.380 153.820 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 0.006974 0.004027 0.000000 0.00000 SCALE2 0.000000 0.008053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006501 0.00000