HEADER OXIDOREDUCTASE 19-SEP-17 6EJ1 TITLE CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ48A. 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: BACULOVIRUSE; 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 6EJ1 0 JRNL AUTH V.SRIKANNATHASAN JRNL TITL CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH KDOPZ48A. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57048 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 2788 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 71.6478 - 5.6181 1.00 2983 149 0.1863 0.1929 REMARK 3 2 5.6181 - 4.4594 1.00 2800 148 0.1515 0.1659 REMARK 3 3 4.4594 - 3.8958 1.00 2752 151 0.1537 0.1643 REMARK 3 4 3.8958 - 3.5396 1.00 2738 160 0.1704 0.1922 REMARK 3 5 3.5396 - 3.2859 1.00 2714 141 0.1988 0.2194 REMARK 3 6 3.2859 - 3.0922 1.00 2715 138 0.2094 0.2452 REMARK 3 7 3.0922 - 2.9373 1.00 2725 141 0.2167 0.2708 REMARK 3 8 2.9373 - 2.8094 1.00 2683 137 0.2213 0.2582 REMARK 3 9 2.8094 - 2.7013 1.00 2681 158 0.2193 0.2628 REMARK 3 10 2.7013 - 2.6081 1.00 2687 131 0.2280 0.2709 REMARK 3 11 2.6081 - 2.5265 1.00 2712 130 0.2200 0.2548 REMARK 3 12 2.5265 - 2.4543 1.00 2678 148 0.2154 0.2529 REMARK 3 13 2.4543 - 2.3897 1.00 2675 113 0.2182 0.2591 REMARK 3 14 2.3897 - 2.3314 1.00 2728 116 0.2238 0.2485 REMARK 3 15 2.3314 - 2.2784 1.00 2640 147 0.2263 0.2301 REMARK 3 16 2.2784 - 2.2299 1.00 2687 127 0.2481 0.2769 REMARK 3 17 2.2299 - 2.1853 1.00 2694 121 0.2556 0.3006 REMARK 3 18 2.1853 - 2.1440 1.00 2649 144 0.2630 0.3054 REMARK 3 19 2.1440 - 2.1057 1.00 2649 140 0.2729 0.2723 REMARK 3 20 2.1057 - 2.0700 1.00 2670 148 0.2761 0.3052 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.79 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 : 0.009 3796 REMARK 3 ANGLE : 0.977 5172 REMARK 3 CHIRALITY : 0.058 551 REMARK 3 PLANARITY : 0.007 692 REMARK 3 DIHEDRAL : 4.562 3094 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): 77.4629 66.8529 11.9931 REMARK 3 T TENSOR REMARK 3 T11: 0.2343 T22: 0.4056 REMARK 3 T33: 0.2669 T12: -0.0126 REMARK 3 T13: 0.0239 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 1.5586 L22: 0.4108 REMARK 3 L33: 0.2009 L12: 0.1944 REMARK 3 L13: 0.2371 L23: -0.0515 REMARK 3 S TENSOR REMARK 3 S11: -0.0442 S12: 0.0591 S13: 0.0816 REMARK 3 S21: -0.0087 S22: 0.0450 S23: 0.0293 REMARK 3 S31: 0.0136 S32: 0.0917 S33: -0.0030 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 6EJ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-17 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 : 57111 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 71.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.30 REMARK 200 R MERGE FOR SHELL (I) : 2.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 71.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.31 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: 1600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 GLY A 370 REMARK 465 GLY A 371 REMARK 465 GLY A 372 REMARK 465 GLY A 373 REMARK 465 GLY A 374 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 ARG A 98 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 375 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 408 CE NZ REMARK 470 LYS A 432 CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 LYS A 446 NZ 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 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 O SER A 431 O HOH A 901 2.03 REMARK 500 OG SER A 431 O GLU A 433 2.04 REMARK 500 O HOH A 921 O HOH A 1061 2.13 REMARK 500 OG SER A 707 O HOH A 902 2.15 REMARK 500 O HOH A 1037 O HOH A 1087 2.16 REMARK 500 O HOH A 1096 O HOH A 1113 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 584 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 584 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 79.86 -110.29 REMARK 500 LEU A 93 -1.09 71.00 REMARK 500 ASP A 420 62.91 -116.15 REMARK 500 SER A 431 -146.28 -149.16 REMARK 500 PHE A 434 -55.72 -121.38 REMARK 500 LEU A 472 2.44 -66.02 REMARK 500 ALA A 473 -78.39 -61.72 REMARK 500 HIS A 474 1.89 -66.63 REMARK 500 ASP A 478 109.99 -59.15 REMARK 500 CYS A 480 -54.29 63.35 REMARK 500 PHE A 493 -3.98 77.37 REMARK 500 ALA A 538 75.32 -151.77 REMARK 500 PHE A 700 -50.97 -149.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 432 GLU A 433 132.47 REMARK 500 GLU A 433 PHE A 434 36.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1144 DISTANCE = 6.59 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 802 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 91 OD1 REMARK 620 2 THR A 416 O 127.4 REMARK 620 N 1 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 OE1 96.4 REMARK 620 3 HIS A 587 NE2 90.1 86.3 REMARK 620 4 B7Q A 807 N2 95.3 165.8 101.6 REMARK 620 5 HOH A 999 O 89.8 91.4 177.6 80.8 REMARK 620 6 HOH A 946 O 177.6 81.5 91.0 86.6 89.1 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 107.7 REMARK 620 3 CYS A 715 SG 118.5 111.4 REMARK 620 4 HIS A 718 ND1 110.1 110.6 98.3 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 DMS 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 B7Q A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 DBREF 6EJ1 A 26 98 UNP Q9UGL1 KDM5B_HUMAN 26 98 DBREF 6EJ1 A 375 754 UNP Q9UGL1 KDM5B_HUMAN 375 754 SEQADV 6EJ1 MET A 25 UNP Q9UGL1 INITIATING METHIONINE SEQADV 6EJ1 GLY A 370 UNP Q9UGL1 LINKER SEQADV 6EJ1 GLY A 371 UNP Q9UGL1 LINKER SEQADV 6EJ1 GLY A 372 UNP Q9UGL1 LINKER SEQADV 6EJ1 GLY A 373 UNP Q9UGL1 LINKER SEQADV 6EJ1 GLY A 374 UNP Q9UGL1 LINKER SEQRES 1 A 459 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 2 A 459 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS SEQRES 3 A 459 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS SEQRES 4 A 459 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 5 A 459 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG SEQRES 6 A 459 LEU ASN GLU LEU GLU ALA GLN THR ARG GLY GLY GLY GLY SEQRES 7 A 459 GLY ARG ASP TYR THR LEU ARG THR PHE GLY GLU MET ALA SEQRES 8 A 459 ASP ALA PHE LYS SER ASP TYR PHE ASN MET PRO VAL HIS SEQRES 9 A 459 MET VAL PRO THR GLU LEU VAL GLU LYS GLU PHE TRP ARG SEQRES 10 A 459 LEU VAL SER THR ILE GLU GLU ASP VAL THR VAL GLU TYR SEQRES 11 A 459 GLY ALA ASP ILE ALA SER LYS GLU PHE GLY SER GLY PHE SEQRES 12 A 459 PRO VAL ARG ASP GLY LYS ILE LYS LEU SER PRO GLU GLU SEQRES 13 A 459 GLU GLU TYR LEU ASP SER GLY TRP ASN LEU ASN ASN MET SEQRES 14 A 459 PRO VAL MET GLU GLN SER VAL LEU ALA HIS ILE THR ALA SEQRES 15 A 459 ASP ILE CYS GLY MET LYS LEU PRO TRP LEU TYR VAL GLY SEQRES 16 A 459 MET CYS PHE SER SER PHE CYS TRP HIS ILE GLU ASP HIS SEQRES 17 A 459 TRP SER TYR SER ILE ASN TYR LEU HIS TRP GLY GLU PRO SEQRES 18 A 459 LYS THR TRP TYR GLY VAL PRO GLY TYR ALA ALA GLU GLN SEQRES 19 A 459 LEU GLU ASN VAL MET LYS LYS LEU ALA PRO GLU LEU PHE SEQRES 20 A 459 VAL SER GLN PRO ASP LEU LEU HIS GLN LEU VAL THR ILE SEQRES 21 A 459 MET ASN PRO ASN THR LEU MET THR HIS GLU VAL PRO VAL SEQRES 22 A 459 TYR ARG THR ASN GLN CYS ALA GLY GLU PHE VAL ILE THR SEQRES 23 A 459 PHE PRO ARG ALA TYR HIS SER GLY PHE ASN GLN GLY PHE SEQRES 24 A 459 ASN PHE ALA GLU ALA VAL ASN PHE CYS THR VAL ASP TRP SEQRES 25 A 459 LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS TYR ARG LEU SEQRES 26 A 459 LEU HIS ARG TYR CYS VAL PHE SER HIS ASP GLU MET ILE SEQRES 27 A 459 CYS LYS MET ALA SER LYS ALA ASP VAL LEU ASP VAL VAL SEQRES 28 A 459 VAL ALA SER THR VAL GLN LYS ASP MET ALA ILE MET ILE SEQRES 29 A 459 GLU ASP GLU LYS ALA LEU ARG GLU THR VAL ARG LYS LEU SEQRES 30 A 459 GLY VAL ILE ASP SER GLU ARG MET ASP PHE GLU LEU LEU SEQRES 31 A 459 PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS LYS THR THR SEQRES 32 A 459 CYS PHE MET SER ALA ILE SER CYS SER CYS LYS PRO GLY SEQRES 33 A 459 LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU LEU CYS SER SEQRES 34 A 459 CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR ARG TYR THR SEQRES 35 A 459 LEU ASP ASP LEU TYR PRO MET MET ASN ALA LEU LYS LEU SEQRES 36 A 459 ARG ALA GLU SER HET ZN A 801 1 HET MN A 802 1 HET MN A 803 1 HET DMS A 804 4 HET DMS A 805 4 HET DMS A 806 4 HET B7Q A 807 30 HET EDO A 808 4 HET EDO A 809 4 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM B7Q 5-[1-[1-(2-CHLORANYLETHANOYL)PIPERIDIN-4-YL]PYRAZOL-4- HETNAM 2 B7Q YL]-7-OXIDANYLIDENE-6-PROPAN-2-YL-4~{H}-PYRAZOLO[1,5- HETNAM 3 B7Q A]PYRIMIDINE-3-CARBONITRILE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MN 2(MN 2+) FORMUL 5 DMS 3(C2 H6 O S) FORMUL 8 B7Q C20 H22 CL N7 O2 FORMUL 9 EDO 2(C2 H6 O2) FORMUL 11 HOH *244(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 GLU A 501 SER A 505 5 5 HELIX 9 AA9 PRO A 523 TYR A 525 5 3 HELIX 10 AB1 ALA A 526 ALA A 538 1 13 HELIX 11 AB2 PRO A 539 VAL A 543 5 5 HELIX 12 AB3 ASN A 557 HIS A 564 1 8 HELIX 13 AB4 THR A 604 ASP A 606 5 3 HELIX 14 AB5 TRP A 607 HIS A 622 1 16 HELIX 15 AB6 SER A 628 LYS A 639 1 12 HELIX 16 AB7 ALA A 640 LEU A 643 5 4 HELIX 17 AB8 ASP A 644 LEU A 672 1 29 HELIX 18 AB9 ASP A 681 LEU A 685 5 5 HELIX 19 AC1 PRO A 686 ARG A 690 5 5 HELIX 20 AC2 HIS A 718 LEU A 722 5 5 HELIX 21 AC3 PRO A 726 TYR A 728 5 3 HELIX 22 AC4 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 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 SSBOND 1 CYS A 708 CYS A 725 1555 1555 2.05 LINK OD1 ASN A 91 MN MN A 802 1555 1555 2.58 LINK O THR A 416 MN MN A 802 1555 1555 2.70 LINK NE2 HIS A 499 MN MN A 803 1555 1555 2.12 LINK OE1 GLU A 501 MN MN A 803 1555 1555 2.00 LINK NE2 HIS A 587 MN MN A 803 1555 1555 2.20 LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.31 LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.36 LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.28 LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.07 LINK MN MN A 803 N2 B7Q A 807 1555 1555 2.18 LINK MN MN A 803 O HOH A 999 1555 1555 2.14 LINK MN MN A 803 O HOH A 946 1555 1555 2.07 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 THR A 416 SITE 2 AC2 5 GLU A 419 SITE 1 AC3 6 HIS A 499 GLU A 501 HIS A 587 B7Q A 807 SITE 2 AC3 6 HOH A 946 HOH A 999 SITE 1 AC4 6 TRP A 486 TYR A 488 GLU A 501 SER A 507 SITE 2 AC4 6 ALA A 599 ASN A 601 SITE 1 AC5 8 ILE A 500 TRP A 504 HIS A 617 TYR A 618 SITE 2 AC5 8 ARG A 623 HOH A 910 HOH A 914 HOH A 929 SITE 1 AC6 5 GLU A 631 GLU A 683 PHE A 700 ARG A 735 SITE 2 AC6 5 TYR A 736 SITE 1 AC7 16 ARG A 98 TYR A 425 GLY A 426 TRP A 486 SITE 2 AC7 16 TYR A 488 PHE A 496 HIS A 499 ASN A 509 SITE 3 AC7 16 LYS A 517 HIS A 587 ASN A 591 MN A 803 SITE 4 AC7 16 EDO A 808 HOH A 946 HOH A 999 HOH A1072 SITE 1 AC8 3 CYS A 497 B7Q A 807 HOH A1072 SITE 1 AC9 6 PHE A 83 GLY A 426 ALA A 427 PHE A 434 SITE 2 AC9 6 LEU A 487 VAL A 489 CRYST1 143.210 143.210 153.820 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 0.006983 0.004031 0.000000 0.00000 SCALE2 0.000000 0.008063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006501 0.00000