HEADER OXIDOREDUCTASE 10-APR-19 6RBI TITLE CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH 5-(1H-TETRAZOL-5-YL) TITLE 2 QUINOLIN-8-OL 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: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS EPIGENETICS, KDM, LYSINE DEMETHYLASE, CHROMATIN, 2-OXOGLUTARATE- KEYWDS 2 DEPENDENT OXYGENASE, TETRAZOLE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.JOHANSSON,J.A.NEWMAN,A.KAWAMURA,C.J.SCHOFIELD,C.H.ARROWSMITH, AUTHOR 2 C.BOUNTRA,A.EDWARDS,U.C.T.OPPERMANN REVDAT 2 24-JAN-24 6RBI 1 LINK REVDAT 1 13-MAY-20 6RBI 0 JRNL AUTH C.JOHANSSON,J.A.NEWMAN,A.KAWAMURA,C.J.SCHOFIELD, JRNL AUTH 2 C.H.ARROWSMITH,C.BOUNTRA,A.EDWARDS,U.C.T.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF KDM5B IN COMPLEX WITH JRNL TITL 2 5-(1H-TETRAZOL-5-YL)QUINOLIN-8-OL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.21 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45679 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2230 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 46.7426 - 5.5660 1.00 2974 137 0.1862 0.1950 REMARK 3 2 5.5660 - 4.4190 1.00 2785 153 0.1421 0.1562 REMARK 3 3 4.4190 - 3.8607 1.00 2751 149 0.1410 0.1458 REMARK 3 4 3.8607 - 3.5079 1.00 2759 128 0.1656 0.1726 REMARK 3 5 3.5079 - 3.2565 1.00 2723 126 0.1923 0.2280 REMARK 3 6 3.2565 - 3.0646 1.00 2718 139 0.1989 0.2131 REMARK 3 7 3.0646 - 2.9111 1.00 2678 148 0.2079 0.2429 REMARK 3 8 2.9111 - 2.7844 1.00 2688 143 0.2040 0.2637 REMARK 3 9 2.7844 - 2.6772 1.00 2695 137 0.2186 0.2464 REMARK 3 10 2.6772 - 2.5848 1.00 2662 150 0.2184 0.2329 REMARK 3 11 2.5848 - 2.5040 1.00 2674 131 0.2207 0.2432 REMARK 3 12 2.5040 - 2.4325 1.00 2694 133 0.2237 0.2459 REMARK 3 13 2.4325 - 2.3684 1.00 2640 147 0.2468 0.2544 REMARK 3 14 2.3684 - 2.3106 1.00 2676 148 0.2471 0.2839 REMARK 3 15 2.3106 - 2.2581 1.00 2653 130 0.2739 0.3223 REMARK 3 16 2.2581 - 2.2101 1.00 2679 131 0.2900 0.3034 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.05 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 : 0.004 3823 REMARK 3 ANGLE : 0.668 5205 REMARK 3 CHIRALITY : 0.045 555 REMARK 3 PLANARITY : 0.005 688 REMARK 3 DIHEDRAL : 12.747 2280 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): 87.4898 67.0019 14.9879 REMARK 3 T TENSOR REMARK 3 T11: 0.2421 T22: 0.4473 REMARK 3 T33: 0.3293 T12: -0.0850 REMARK 3 T13: 0.0303 T23: -0.0626 REMARK 3 L TENSOR REMARK 3 L11: 2.1918 L22: 1.9841 REMARK 3 L33: 2.9140 L12: -0.3347 REMARK 3 L13: 0.4044 L23: -0.3883 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: -0.0735 S13: 0.0364 REMARK 3 S21: -0.0033 S22: 0.0218 S23: 0.0853 REMARK 3 S31: 0.2434 S32: -0.1462 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 754 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.4978 64.2606 5.4105 REMARK 3 T TENSOR REMARK 3 T11: 0.1762 T22: 0.3944 REMARK 3 T33: 0.3550 T12: 0.0126 REMARK 3 T13: -0.0164 T23: 0.0366 REMARK 3 L TENSOR REMARK 3 L11: 2.0305 L22: 3.6665 REMARK 3 L33: 3.8933 L12: 0.8832 REMARK 3 L13: 0.4357 L23: 1.7567 REMARK 3 S TENSOR REMARK 3 S11: -0.1372 S12: 0.0258 S13: 0.0887 REMARK 3 S21: -0.0325 S22: 0.1705 S23: 0.1734 REMARK 3 S31: -0.0001 S32: 0.2793 S33: -0.0214 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 6RBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-18 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) : 0.97628 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45740 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 47.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.20 REMARK 200 R MERGE FOR SHELL (I) : 2.49500 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: PHASER 2.8.0 REMARK 200 STARTING MODEL: 5FUN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.8 M POTASSIUM REMARK 280 PHOSPHATE-DIBASIC, 0.8 M 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 101.02667 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 50.51333 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 75.77000 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 25.25667 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 126.28333 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 101.02667 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 50.51333 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 25.25667 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 75.77000 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 126.28333 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: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 HOH A 912 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1013 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 SER A 24 REMARK 465 GLY A 370 REMARK 465 GLY A 371 REMARK 465 GLY A 372 REMARK 465 GLY A 373 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 REMARK 465 ILE A 445 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 LYS A 51 CD CE NZ REMARK 470 GLN A 71 CG CD OE1 NE2 REMARK 470 ARG A 86 CZ NH1 NH2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LEU A 101 CG CD1 CD2 REMARK 470 LYS A 408 CE NZ REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CD OE1 OE2 REMARK 470 LYS A 446 CG CD CE NZ REMARK 470 GLU A 451 CD OE1 OE2 REMARK 470 ASP A 456 CG OD1 OD2 REMARK 470 LYS A 483 CD CE NZ REMARK 470 GLU A 528 CD OE1 OE2 REMARK 470 LYS A 535 CE NZ REMARK 470 LYS A 536 CE NZ REMARK 470 ASP A 547 OD1 OD2 REMARK 470 GLU A 565 CG CD OE1 OE2 REMARK 470 LYS A 639 CE NZ REMARK 470 LYS A 653 CE NZ REMARK 470 GLU A 660 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 N MET A 25 O HOH A 901 2.12 REMARK 500 NE ARG A 86 O HOH A 902 2.16 REMARK 500 O GLU A 453 O HOH A 903 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 43 -71.75 -49.97 REMARK 500 PHE A 434 99.75 -163.82 REMARK 500 GLU A 451 47.20 -81.25 REMARK 500 ILE A 479 56.94 -114.43 REMARK 500 PHE A 493 -7.89 81.42 REMARK 500 PHE A 700 -53.36 -150.60 REMARK 500 GLU A 753 44.02 -88.84 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 NA A 810 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 91 OD1 REMARK 620 2 LEU A 413 O 134.0 REMARK 620 3 THR A 416 O 134.9 84.3 REMARK 620 4 GLU A 419 O 97.3 115.9 79.6 REMARK 620 5 HOH A 967 O 76.4 85.9 139.4 69.7 REMARK 620 6 HOH A1012 O 72.6 108.6 72.5 124.0 147.3 REMARK 620 N 1 2 3 4 5 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 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 84.6 REMARK 620 3 JX8 A 805 O 90.0 81.0 REMARK 620 4 JX8 A 805 N4 95.8 167.0 86.0 REMARK 620 5 HOH A 985 O 90.4 100.6 178.3 92.3 REMARK 620 6 HOH A 996 O 176.9 92.4 90.6 87.3 89.0 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 106.7 REMARK 620 3 CYS A 715 SG 114.7 113.9 REMARK 620 4 HIS A 718 ND1 109.4 108.7 103.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 809 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 706 SG REMARK 620 2 CYS A 708 SG 113.4 REMARK 620 3 CYS A 723 SG 110.6 112.8 REMARK 620 4 CYS A 725 SG 103.1 108.2 108.1 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 PO4 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JX8 A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 ZN A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 811 DBREF 6RBI A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 6RBI A 374 772 UNP Q9UGL1 KDM5B_HUMAN 374 772 SEQADV 6RBI SER A 24 UNP Q9UGL1 EXPRESSION TAG SEQADV 6RBI MET A 25 UNP Q9UGL1 EXPRESSION TAG SEQADV 6RBI GLY A 370 UNP Q9UGL1 LINKER SEQADV 6RBI GLY A 371 UNP Q9UGL1 LINKER SEQADV 6RBI GLY A 372 UNP Q9UGL1 LINKER SEQADV 6RBI GLY A 373 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 A 801 1 HET MN A 802 1 HET PO4 A 803 5 HET EDO A 804 4 HET JX8 A 805 16 HET EDO A 806 4 HET EDO A 807 4 HET EDO A 808 4 HET ZN A 809 1 HET NA A 810 1 HET NA A 811 1 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM JX8 5-(1~{H}-1,2,3,4-TETRAZOL-5-YL)QUINOLIN-8-OL HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 3 MN MN 2+ FORMUL 4 PO4 O4 P 3- FORMUL 5 EDO 4(C2 H6 O2) FORMUL 6 JX8 C10 H7 N5 O FORMUL 11 NA 2(NA 1+) FORMUL 13 HOH *126(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 402 VAL A 414 1 13 HELIX 5 AA5 ASN A 460 MET A 464 5 5 HELIX 6 AA6 SER A 470 ILE A 475 5 6 HELIX 7 AA7 ILE A 479 LEU A 484 1 6 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 ASP A 547 HIS A 550 5 4 HELIX 13 AB4 ASN A 557 HIS A 564 1 8 HELIX 14 AB5 THR A 604 ASP A 606 5 3 HELIX 15 AB6 TRP A 607 HIS A 622 1 16 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 CYS A 715 LEU A 722 5 8 HELIX 22 AC4 PRO A 726 TYR A 728 5 3 HELIX 23 AC5 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 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 LINK OD1 ASN A 91 NA NA A 810 1555 1555 2.64 LINK O LEU A 413 NA NA A 810 1555 1555 2.77 LINK O THR A 416 NA NA A 810 1555 1555 2.43 LINK O GLU A 419 NA NA A 810 1555 1555 2.98 LINK NE2 HIS A 499 MN MN A 802 1555 1555 2.18 LINK OE2 GLU A 501 MN MN A 802 1555 1555 2.16 LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.23 LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.39 LINK SG CYS A 706 ZN ZN A 809 1555 1555 2.37 LINK SG CYS A 708 ZN ZN A 809 1555 1555 2.26 LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.34 LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.09 LINK SG CYS A 723 ZN ZN A 809 1555 1555 2.30 LINK SG CYS A 725 ZN ZN A 809 1555 1555 2.55 LINK MN MN A 802 O JX8 A 805 1555 1555 2.03 LINK MN MN A 802 N4 JX8 A 805 1555 1555 1.95 LINK MN MN A 802 O HOH A 985 1555 1555 2.08 LINK MN MN A 802 O HOH A 996 1555 1555 2.37 LINK NA NA A 810 O HOH A 967 1555 1555 2.38 LINK NA NA A 810 O HOH A1012 1555 1555 3.20 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 5 HIS A 499 GLU A 501 JX8 A 805 HOH A 985 SITE 2 AC2 5 HOH A 996 SITE 1 AC3 6 HIS A 622 LYS A 694 HIS A 718 HOH A 904 SITE 2 AC3 6 HOH A 906 HOH A 986 SITE 1 AC4 7 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AC4 7 VAL A 693 GLY A 711 LEU A 713 SITE 1 AC5 14 TYR A 488 PHE A 496 HIS A 499 GLU A 501 SITE 2 AC5 14 LYS A 517 TRP A 519 HIS A 587 ASN A 591 SITE 3 AC5 14 MN A 802 HOH A 973 HOH A 985 HOH A 996 SITE 4 AC5 14 HOH A1000 HOH A1005 SITE 1 AC6 3 GLY A 524 ARG A 584 HOH A1002 SITE 1 AC7 2 CYS A 497 HOH A 908 SITE 1 AC8 5 GLU A 631 LYS A 635 GLU A 683 PHE A 700 SITE 2 AC8 5 TYR A 736 SITE 1 AC9 4 CYS A 706 CYS A 708 CYS A 723 CYS A 725 SITE 1 AD1 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AD1 6 GLU A 419 HOH A 967 SITE 1 AD2 1 TYR A 618 CRYST1 142.150 142.150 151.540 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007035 0.004062 0.000000 0.00000 SCALE2 0.000000 0.008123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006599 0.00000