HEADER OXIDOREDUCTASE 10-APR-19 6RBJ TITLE CRYSTAL STRUCTURE OF KDM3B IN COMPLEX WITH 5-(1H-TETRAZOL-5-YL) TITLE 2 QUINOLIN-8-OL COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 3B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 2B, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 1B,NUCLEAR PROTEIN 5QNCA; COMPND 6 EC: 1.14.11.-; COMPND 7 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: KDM3B, C5ORF7, JHDM2B, JMJD1B, KIAA1082; 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 6RBJ 1 LINK REVDAT 1 13-MAY-20 6RBJ 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 KDM3B 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. 2.09 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 86.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 53226 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2610 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 86.4775 - 5.5848 0.98 2718 138 0.1742 0.1734 REMARK 3 2 5.5848 - 4.4328 1.00 2694 142 0.1393 0.1636 REMARK 3 3 4.4328 - 3.8725 1.00 2686 132 0.1392 0.1394 REMARK 3 4 3.8725 - 3.5184 0.99 2653 132 0.1638 0.1774 REMARK 3 5 3.5184 - 3.2662 0.99 2690 115 0.1903 0.2298 REMARK 3 6 3.2662 - 3.0737 0.99 2709 129 0.1991 0.2254 REMARK 3 7 3.0737 - 2.9197 1.00 2641 140 0.2037 0.2165 REMARK 3 8 2.9197 - 2.7926 0.99 2669 133 0.2097 0.2241 REMARK 3 9 2.7926 - 2.6851 1.00 2649 142 0.2140 0.2404 REMARK 3 10 2.6851 - 2.5924 1.00 2654 133 0.2203 0.2563 REMARK 3 11 2.5924 - 2.5114 1.00 2682 128 0.2223 0.2715 REMARK 3 12 2.5114 - 2.4396 1.00 2693 131 0.2156 0.2635 REMARK 3 13 2.4396 - 2.3754 1.00 2601 141 0.2113 0.2309 REMARK 3 14 2.3754 - 2.3174 1.00 2667 167 0.2110 0.2045 REMARK 3 15 2.3174 - 2.2647 1.00 2644 142 0.2186 0.2589 REMARK 3 16 2.2647 - 2.2165 1.00 2668 142 0.2290 0.2591 REMARK 3 17 2.2165 - 2.1722 0.99 2615 155 0.2608 0.2873 REMARK 3 18 2.1722 - 2.1312 0.99 2672 115 0.2986 0.3431 REMARK 3 19 2.1312 - 2.0931 0.98 2611 153 0.3263 0.3836 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) : 22.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.12 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 5571 REMARK 3 ANGLE : 0.566 7555 REMARK 3 CHIRALITY : 0.044 796 REMARK 3 PLANARITY : 0.003 1023 REMARK 3 DIHEDRAL : 14.375 3334 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1378 THROUGH 1493 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.3089 74.9212 125.6598 REMARK 3 T TENSOR REMARK 3 T11: 0.2045 T22: 0.2190 REMARK 3 T33: 0.1531 T12: -0.0324 REMARK 3 T13: -0.0067 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.7714 L22: 6.9387 REMARK 3 L33: 0.7188 L12: -0.6535 REMARK 3 L13: 0.0692 L23: -0.4751 REMARK 3 S TENSOR REMARK 3 S11: -0.0330 S12: -0.0608 S13: -0.0897 REMARK 3 S21: 0.1243 S22: 0.0372 S23: 0.0920 REMARK 3 S31: 0.1327 S32: -0.0464 S33: -0.0095 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1494 THROUGH 1564 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.6539 77.9350 116.8729 REMARK 3 T TENSOR REMARK 3 T11: 0.2350 T22: 0.1630 REMARK 3 T33: 0.2225 T12: -0.0310 REMARK 3 T13: -0.0234 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 0.7886 L22: 2.5540 REMARK 3 L33: 1.6280 L12: -0.3014 REMARK 3 L13: -0.0874 L23: -0.7309 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: 0.0924 S13: -0.1807 REMARK 3 S21: -0.0968 S22: 0.0075 S23: 0.3226 REMARK 3 S31: 0.2044 S32: -0.1531 S33: -0.0550 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1565 THROUGH 1717 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8052 82.5387 119.7481 REMARK 3 T TENSOR REMARK 3 T11: 0.1877 T22: 0.1180 REMARK 3 T33: 0.1969 T12: 0.0020 REMARK 3 T13: 0.0009 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 2.2917 L22: 2.2873 REMARK 3 L33: 2.1628 L12: -0.2113 REMARK 3 L13: 0.1488 L23: -0.6112 REMARK 3 S TENSOR REMARK 3 S11: 0.0215 S12: -0.0007 S13: -0.0549 REMARK 3 S21: 0.0126 S22: -0.1304 S23: -0.2558 REMARK 3 S31: 0.1087 S32: 0.2377 S33: 0.0977 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1380 THROUGH 1493 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.9016 68.6380 76.4120 REMARK 3 T TENSOR REMARK 3 T11: 0.1677 T22: 0.2571 REMARK 3 T33: 0.2658 T12: -0.0200 REMARK 3 T13: 0.0074 T23: -0.0265 REMARK 3 L TENSOR REMARK 3 L11: 1.3239 L22: 4.6929 REMARK 3 L33: 3.5850 L12: -0.8709 REMARK 3 L13: -0.4701 L23: 2.5937 REMARK 3 S TENSOR REMARK 3 S11: 0.0293 S12: 0.0471 S13: 0.0209 REMARK 3 S21: -0.1076 S22: 0.1379 S23: -0.2742 REMARK 3 S31: -0.2588 S32: 0.0904 S33: -0.1705 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1494 THROUGH 1564 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.7191 62.3261 73.7387 REMARK 3 T TENSOR REMARK 3 T11: 0.2020 T22: 0.2587 REMARK 3 T33: 0.2472 T12: 0.0468 REMARK 3 T13: -0.0103 T23: -0.0160 REMARK 3 L TENSOR REMARK 3 L11: 0.4481 L22: 2.7363 REMARK 3 L33: 2.0340 L12: 0.7317 REMARK 3 L13: 0.1311 L23: 1.2884 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0474 S13: 0.1387 REMARK 3 S21: -0.0462 S22: 0.0775 S23: 0.0536 REMARK 3 S31: -0.1946 S32: -0.0535 S33: -0.0356 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1565 THROUGH 1706 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3620 57.2736 82.5895 REMARK 3 T TENSOR REMARK 3 T11: 0.2467 T22: 0.3277 REMARK 3 T33: 0.3469 T12: 0.0530 REMARK 3 T13: -0.0914 T23: -0.0985 REMARK 3 L TENSOR REMARK 3 L11: 2.4373 L22: 2.6110 REMARK 3 L33: 2.8427 L12: 0.2005 REMARK 3 L13: 0.5533 L23: 0.4681 REMARK 3 S TENSOR REMARK 3 S11: 0.0689 S12: -0.2678 S13: -0.1823 REMARK 3 S21: 0.3447 S22: 0.1652 S23: -0.6101 REMARK 3 S31: 0.2446 S32: 0.3946 S33: -0.1518 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1707 THROUGH 1725 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.0950 46.5619 80.0087 REMARK 3 T TENSOR REMARK 3 T11: 0.3431 T22: 0.3308 REMARK 3 T33: 0.2747 T12: -0.0363 REMARK 3 T13: -0.0739 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 3.8780 L22: 7.7860 REMARK 3 L33: 3.7700 L12: 1.9809 REMARK 3 L13: -3.6812 L23: -0.7071 REMARK 3 S TENSOR REMARK 3 S11: 0.0904 S12: -0.2249 S13: -0.3808 REMARK 3 S21: 0.6541 S22: -0.3429 S23: 0.0213 REMARK 3 S31: 0.1007 S32: 0.1824 S33: 0.2418 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 6RBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101774. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 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) : 0.976280 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 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53263 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 86.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.60700 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: 4C8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.6 , 0.1 M REMARK 280 MAGNESIUM CHLORIDE, 28% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 46.87700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ILE A 1577 REMARK 465 GLY A 1578 REMARK 465 GLU A 1579 REMARK 465 GLY A 1580 REMARK 465 ALA A 1581 REMARK 465 GLN A 1718 REMARK 465 GLU A 1719 REMARK 465 PHE A 1720 REMARK 465 ARG A 1721 REMARK 465 HIS A 1722 REMARK 465 LEU A 1723 REMARK 465 SER A 1724 REMARK 465 ASN A 1725 REMARK 465 THR A 1726 REMARK 465 HIS A 1727 REMARK 465 THR A 1728 REMARK 465 SER B 1378 REMARK 465 MET B 1379 REMARK 465 ILE B 1577 REMARK 465 GLY B 1578 REMARK 465 GLU B 1579 REMARK 465 GLY B 1580 REMARK 465 ALA B 1581 REMARK 465 THR B 1726 REMARK 465 HIS B 1727 REMARK 465 THR B 1728 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 LYS A1399 CD CE NZ REMARK 470 LYS A1430 CE NZ REMARK 470 GLU A1432 CD OE1 OE2 REMARK 470 GLN A1436 CD OE1 NE2 REMARK 470 GLU A1476 CG CD OE1 OE2 REMARK 470 LEU A1536 CD1 CD2 REMARK 470 GLU A1550 CD OE1 OE2 REMARK 470 GLU A1584 CG CD OE1 OE2 REMARK 470 GLU A1585 CD OE1 OE2 REMARK 470 LYS A1588 CE NZ REMARK 470 GLU A1592 CD OE1 OE2 REMARK 470 GLU A1634 CD OE1 OE2 REMARK 470 GLU A1639 CB CG CD OE1 OE2 REMARK 470 LYS A1660 CD CE NZ REMARK 470 GLU A1664 OE1 OE2 REMARK 470 LYS B1399 CG CD CE NZ REMARK 470 LYS B1403 NZ REMARK 470 LYS B1410 CE NZ REMARK 470 LYS B1425 NZ REMARK 470 LYS B1471 CE NZ REMARK 470 GLU B1503 CD OE1 OE2 REMARK 470 GLU B1507 CD OE1 OE2 REMARK 470 GLU B1513 OE1 OE2 REMARK 470 ASP B1535 CG OD1 OD2 REMARK 470 GLU B1550 CG CD OE1 OE2 REMARK 470 ARG B1553 CZ NH1 NH2 REMARK 470 HIS B1582 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B1584 CG CD OE1 OE2 REMARK 470 GLU B1585 CG CD OE1 OE2 REMARK 470 LYS B1588 CD CE NZ REMARK 470 GLU B1592 CD OE1 OE2 REMARK 470 GLU B1597 CG CD OE1 OE2 REMARK 470 LYS B1607 NZ REMARK 470 LYS B1620 CE NZ REMARK 470 LYS B1624 NZ REMARK 470 LYS B1631 CG CD CE NZ REMARK 470 GLU B1634 CD OE1 OE2 REMARK 470 GLN B1638 CG CD OE1 NE2 REMARK 470 GLU B1639 CG CD OE1 OE2 REMARK 470 GLN B1656 CG CD OE1 NE2 REMARK 470 LYS B1660 CG CD CE NZ REMARK 470 GLU B1664 CD OE1 OE2 REMARK 470 ARG B1715 NE CZ NH1 NH2 REMARK 470 GLU B1719 OE1 OE2 REMARK 470 ASN B1725 O CG OD1 ND2 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 ILE A1547 -58.07 -122.26 REMARK 500 ASP A1594 35.53 80.12 REMARK 500 ASP B1535 70.61 46.97 REMARK 500 ILE B1547 -63.10 -123.64 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 A1804 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1560 NE2 REMARK 620 2 ASP A1562 OD2 93.5 REMARK 620 3 JX8 A1803 O 99.2 86.9 REMARK 620 4 JX8 A1803 N4 98.4 160.3 75.7 REMARK 620 5 HOH A1931 O 176.4 83.1 81.7 85.2 REMARK 620 6 HOH A1944 O 89.5 103.8 165.8 92.0 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1805 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B1560 NE2 REMARK 620 2 ASP B1562 OD2 96.3 REMARK 620 3 JX8 B1804 O 94.3 81.5 REMARK 620 4 JX8 B1804 N4 95.0 157.5 78.3 REMARK 620 5 HOH B1905 O 92.1 110.6 165.7 88.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JX8 A 1803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 1804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 1801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 1802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 1803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JX8 B 1804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 1805 DBREF 6RBJ A 1380 1728 UNP Q7LBC6 KDM3B_HUMAN 1380 1728 DBREF 6RBJ B 1380 1728 UNP Q7LBC6 KDM3B_HUMAN 1380 1728 SEQADV 6RBJ SER A 1378 UNP Q7LBC6 EXPRESSION TAG SEQADV 6RBJ MET A 1379 UNP Q7LBC6 EXPRESSION TAG SEQADV 6RBJ SER B 1378 UNP Q7LBC6 EXPRESSION TAG SEQADV 6RBJ MET B 1379 UNP Q7LBC6 EXPRESSION TAG SEQRES 1 A 351 SER MET THR SER HIS SER TRP LEU CYS ASP GLY ARG LEU SEQRES 2 A 351 LEU CYS LEU HIS ASP PRO SER ASN LYS ASN ASN TRP LYS SEQRES 3 A 351 ILE PHE ARG GLU CYS TRP LYS GLN GLY GLN PRO VAL LEU SEQRES 4 A 351 VAL SER GLY VAL HIS LYS LYS LEU LYS SER GLU LEU TRP SEQRES 5 A 351 LYS PRO GLU ALA PHE SER GLN GLU PHE GLY ASP GLN ASP SEQRES 6 A 351 VAL ASP LEU VAL ASN CYS ARG ASN CYS ALA ILE ILE SER SEQRES 7 A 351 ASP VAL LYS VAL ARG ASP PHE TRP ASP GLY PHE GLU ILE SEQRES 8 A 351 ILE CYS LYS ARG LEU ARG SER GLU ASP GLY GLN PRO MET SEQRES 9 A 351 VAL LEU LYS LEU LYS ASP TRP PRO PRO GLY GLU ASP PHE SEQRES 10 A 351 ARG ASP MET MET PRO THR ARG PHE GLU ASP LEU MET GLU SEQRES 11 A 351 ASN LEU PRO LEU PRO GLU TYR THR LYS ARG ASP GLY ARG SEQRES 12 A 351 LEU ASN LEU ALA SER ARG LEU PRO SER TYR PHE VAL ARG SEQRES 13 A 351 PRO ASP LEU GLY PRO LYS MET TYR ASN ALA TYR GLY LEU SEQRES 14 A 351 ILE THR ALA GLU ASP ARG ARG VAL GLY THR THR ASN LEU SEQRES 15 A 351 HIS LEU ASP VAL SER ASP ALA VAL ASN VAL MET VAL TYR SEQRES 16 A 351 VAL GLY ILE PRO ILE GLY GLU GLY ALA HIS ASP GLU GLU SEQRES 17 A 351 VAL LEU LYS THR ILE ASP GLU GLY ASP ALA ASP GLU VAL SEQRES 18 A 351 THR LYS GLN ARG ILE HIS ASP GLY LYS GLU LYS PRO GLY SEQRES 19 A 351 ALA LEU TRP HIS ILE TYR ALA ALA LYS ASP ALA GLU LYS SEQRES 20 A 351 ILE ARG GLU LEU LEU ARG LYS VAL GLY GLU GLU GLN GLY SEQRES 21 A 351 GLN GLU ASN PRO PRO ASP HIS ASP PRO ILE HIS ASP GLN SEQRES 22 A 351 SER TRP TYR LEU ASP GLN THR LEU ARG LYS ARG LEU TYR SEQRES 23 A 351 GLU GLU TYR GLY VAL GLN GLY TRP ALA ILE VAL GLN PHE SEQRES 24 A 351 LEU GLY ASP ALA VAL PHE ILE PRO ALA GLY ALA PRO HIS SEQRES 25 A 351 GLN VAL HIS ASN LEU TYR SER CYS ILE LYS VAL ALA GLU SEQRES 26 A 351 ASP PHE VAL SER PRO GLU HIS VAL LYS HIS CYS PHE ARG SEQRES 27 A 351 LEU THR GLN GLU PHE ARG HIS LEU SER ASN THR HIS THR SEQRES 1 B 351 SER MET THR SER HIS SER TRP LEU CYS ASP GLY ARG LEU SEQRES 2 B 351 LEU CYS LEU HIS ASP PRO SER ASN LYS ASN ASN TRP LYS SEQRES 3 B 351 ILE PHE ARG GLU CYS TRP LYS GLN GLY GLN PRO VAL LEU SEQRES 4 B 351 VAL SER GLY VAL HIS LYS LYS LEU LYS SER GLU LEU TRP SEQRES 5 B 351 LYS PRO GLU ALA PHE SER GLN GLU PHE GLY ASP GLN ASP SEQRES 6 B 351 VAL ASP LEU VAL ASN CYS ARG ASN CYS ALA ILE ILE SER SEQRES 7 B 351 ASP VAL LYS VAL ARG ASP PHE TRP ASP GLY PHE GLU ILE SEQRES 8 B 351 ILE CYS LYS ARG LEU ARG SER GLU ASP GLY GLN PRO MET SEQRES 9 B 351 VAL LEU LYS LEU LYS ASP TRP PRO PRO GLY GLU ASP PHE SEQRES 10 B 351 ARG ASP MET MET PRO THR ARG PHE GLU ASP LEU MET GLU SEQRES 11 B 351 ASN LEU PRO LEU PRO GLU TYR THR LYS ARG ASP GLY ARG SEQRES 12 B 351 LEU ASN LEU ALA SER ARG LEU PRO SER TYR PHE VAL ARG SEQRES 13 B 351 PRO ASP LEU GLY PRO LYS MET TYR ASN ALA TYR GLY LEU SEQRES 14 B 351 ILE THR ALA GLU ASP ARG ARG VAL GLY THR THR ASN LEU SEQRES 15 B 351 HIS LEU ASP VAL SER ASP ALA VAL ASN VAL MET VAL TYR SEQRES 16 B 351 VAL GLY ILE PRO ILE GLY GLU GLY ALA HIS ASP GLU GLU SEQRES 17 B 351 VAL LEU LYS THR ILE ASP GLU GLY ASP ALA ASP GLU VAL SEQRES 18 B 351 THR LYS GLN ARG ILE HIS ASP GLY LYS GLU LYS PRO GLY SEQRES 19 B 351 ALA LEU TRP HIS ILE TYR ALA ALA LYS ASP ALA GLU LYS SEQRES 20 B 351 ILE ARG GLU LEU LEU ARG LYS VAL GLY GLU GLU GLN GLY SEQRES 21 B 351 GLN GLU ASN PRO PRO ASP HIS ASP PRO ILE HIS ASP GLN SEQRES 22 B 351 SER TRP TYR LEU ASP GLN THR LEU ARG LYS ARG LEU TYR SEQRES 23 B 351 GLU GLU TYR GLY VAL GLN GLY TRP ALA ILE VAL GLN PHE SEQRES 24 B 351 LEU GLY ASP ALA VAL PHE ILE PRO ALA GLY ALA PRO HIS SEQRES 25 B 351 GLN VAL HIS ASN LEU TYR SER CYS ILE LYS VAL ALA GLU SEQRES 26 B 351 ASP PHE VAL SER PRO GLU HIS VAL LYS HIS CYS PHE ARG SEQRES 27 B 351 LEU THR GLN GLU PHE ARG HIS LEU SER ASN THR HIS THR HET EDO A1801 10 HET EDO A1802 10 HET JX8 A1803 23 HET MN A1804 1 HET CL A1805 1 HET EDO B1801 10 HET EDO B1802 10 HET EDO B1803 10 HET JX8 B1804 23 HET MN B1805 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM JX8 5-(1~{H}-1,2,3,4-TETRAZOL-5-YL)QUINOLIN-8-OL HETNAM MN MANGANESE (II) ION HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 5(C2 H6 O2) FORMUL 5 JX8 2(C10 H7 N5 O) FORMUL 6 MN 2(MN 2+) FORMUL 7 CL CL 1- FORMUL 13 HOH *130(H2 O) HELIX 1 AA1 CYS A 1386 ARG A 1389 5 4 HELIX 2 AA2 ASN A 1400 LYS A 1410 1 11 HELIX 3 AA3 GLY A 1419 LEU A 1424 5 6 HELIX 4 AA4 LYS A 1425 TRP A 1429 5 5 HELIX 5 AA5 LYS A 1430 GLY A 1439 1 10 HELIX 6 AA6 VAL A 1459 ASP A 1464 1 6 HELIX 7 AA7 ILE A 1468 ARG A 1472 5 5 HELIX 8 AA8 ASP A 1493 MET A 1498 1 6 HELIX 9 AA9 MET A 1498 GLU A 1507 1 10 HELIX 10 AB1 LEU A 1511 LYS A 1516 1 6 HELIX 11 AB2 LEU A 1523 LEU A 1527 5 5 HELIX 12 AB3 ALA A 1549 VAL A 1554 5 6 HELIX 13 AB4 ASP A 1583 GLY A 1593 1 11 HELIX 14 AB5 ASP A 1596 ASP A 1605 1 10 HELIX 15 AB6 ALA A 1618 LYS A 1620 5 3 HELIX 16 AB7 ASP A 1621 GLN A 1636 1 16 HELIX 17 AB8 ASP A 1645 GLN A 1650 1 6 HELIX 18 AB9 ASP A 1655 GLY A 1667 1 13 HELIX 19 AC1 SER A 1706 PHE A 1714 5 9 HELIX 20 AC2 ASN B 1401 GLN B 1411 1 11 HELIX 21 AC3 GLY B 1419 LEU B 1424 5 6 HELIX 22 AC4 LYS B 1425 TRP B 1429 5 5 HELIX 23 AC5 LYS B 1430 GLY B 1439 1 10 HELIX 24 AC6 VAL B 1459 ASP B 1464 1 6 HELIX 25 AC7 ILE B 1468 ARG B 1472 5 5 HELIX 26 AC8 ASP B 1493 MET B 1498 1 6 HELIX 27 AC9 MET B 1498 GLU B 1507 1 10 HELIX 28 AD1 LEU B 1511 LYS B 1516 1 6 HELIX 29 AD2 ALA B 1549 VAL B 1554 5 6 HELIX 30 AD3 ASP B 1583 GLY B 1593 1 11 HELIX 31 AD4 ASP B 1596 ASP B 1605 1 10 HELIX 32 AD5 ALA B 1618 LYS B 1620 5 3 HELIX 33 AD6 ASP B 1621 GLY B 1637 1 17 HELIX 34 AD7 ASP B 1645 GLN B 1650 1 6 HELIX 35 AD8 ASP B 1655 GLY B 1667 1 13 HELIX 36 AD9 SER B 1706 GLU B 1708 5 3 HELIX 37 AE1 HIS B 1709 SER B 1724 1 16 SHEET 1 AA110 HIS A1382 LEU A1385 0 SHEET 2 AA110 LEU A1390 LEU A1393 -1 O LEU A1390 N LEU A1385 SHEET 3 AA110 VAL A1415 VAL A1417 1 O LEU A1416 N LEU A1393 SHEET 4 AA110 ALA A1680 ILE A1683 -1 O ALA A1680 N VAL A1417 SHEET 5 AA110 ASP A1565 GLY A1574 -1 N ASN A1568 O VAL A1681 SHEET 6 AA110 SER A1696 PHE A1704 -1 O VAL A1700 N VAL A1569 SHEET 7 AA110 LYS A1539 ALA A1543 -1 N TYR A1541 O LYS A1699 SHEET 8 AA110 LEU A1483 LYS A1486 -1 N LEU A1485 O ASN A1542 SHEET 9 AA110 ASP A1442 ASN A1447 -1 N VAL A1446 O LYS A1484 SHEET 10 AA110 ILE A1453 LYS A1458 -1 O ILE A1454 N LEU A1445 SHEET 1 AA2 4 THR A1557 HIS A1560 0 SHEET 2 AA2 4 HIS A1689 ASN A1693 -1 O HIS A1689 N HIS A1560 SHEET 3 AA2 4 PRO A1610 ILE A1616 -1 N LEU A1613 O HIS A1692 SHEET 4 AA2 4 TRP A1671 PHE A1676 -1 O ILE A1673 N TRP A1614 SHEET 1 AA310 HIS B1382 LEU B1385 0 SHEET 2 AA310 LEU B1390 LEU B1393 -1 O CYS B1392 N SER B1383 SHEET 3 AA310 VAL B1415 VAL B1417 1 O LEU B1416 N LEU B1393 SHEET 4 AA310 ALA B1680 ILE B1683 -1 O ALA B1680 N VAL B1417 SHEET 5 AA310 ASP B1565 GLY B1574 -1 N ASN B1568 O VAL B1681 SHEET 6 AA310 SER B1696 PHE B1704 -1 O VAL B1700 N VAL B1569 SHEET 7 AA310 LYS B1539 ALA B1543 -1 N TYR B1541 O LYS B1699 SHEET 8 AA310 LEU B1483 LYS B1486 -1 N LEU B1485 O ASN B1542 SHEET 9 AA310 ASP B1442 ASN B1447 -1 N VAL B1446 O LYS B1484 SHEET 10 AA310 ILE B1453 LYS B1458 -1 O ILE B1454 N LEU B1445 SHEET 1 AA4 4 THR B1557 HIS B1560 0 SHEET 2 AA4 4 HIS B1689 ASN B1693 -1 O HIS B1689 N HIS B1560 SHEET 3 AA4 4 PRO B1610 ILE B1616 -1 N LEU B1613 O HIS B1692 SHEET 4 AA4 4 TRP B1671 PHE B1676 -1 O ILE B1673 N TRP B1614 LINK NE2 HIS A1560 MN MN A1804 1555 1555 2.19 LINK OD2 ASP A1562 MN MN A1804 1555 1555 2.34 LINK O JX8 A1803 MN MN A1804 1555 1555 2.08 LINK N4 JX8 A1803 MN MN A1804 1555 1555 2.32 LINK MN MN A1804 O HOH A1931 1555 1555 2.09 LINK MN MN A1804 O HOH A1944 1555 1555 2.13 LINK NE2 HIS B1560 MN MN B1805 1555 1555 2.27 LINK OD2 ASP B1562 MN MN B1805 1555 1555 2.29 LINK O JX8 B1804 MN MN B1805 1555 1555 1.99 LINK N4 JX8 B1804 MN MN B1805 1555 1555 2.29 LINK MN MN B1805 O HOH B1905 1555 1555 2.09 CISPEP 1 TRP A 1488 PRO A 1489 0 -6.39 CISPEP 2 TRP B 1488 PRO B 1489 0 -7.13 SITE 1 AC1 5 ARG A1552 THR A1589 GLY A1593 TYR A1653 SITE 2 AC1 5 ARG A1659 SITE 1 AC2 4 LEU A1485 ASP A1487 TYR A1541 HOH A1957 SITE 1 AC3 13 TYR A1541 THR A1557 HIS A1560 ASP A1562 SITE 2 AC3 13 ASN A1568 TRP A1614 HIS A1689 VAL A1691 SITE 3 AC3 13 LYS A1699 MN A1804 HOH A1931 HOH A1937 SITE 4 AC3 13 HOH A1978 SITE 1 AC4 5 HIS A1560 ASP A1562 JX8 A1803 HOH A1931 SITE 2 AC4 5 HOH A1944 SITE 1 AC5 3 LEU A1511 PRO A1512 GLU A1513 SITE 1 AC6 5 GLY B1537 ALA B1701 GLU B1702 ASP B1703 SITE 2 AC6 5 HOH B1922 SITE 1 AC7 4 ASP B1442 VAL B1443 ASP B1444 ASP B1456 SITE 1 AC8 6 ARG A1715 ASN B1447 ASN B1450 ALA B1452 SITE 2 AC8 6 SER B1475 GLU B1476 SITE 1 AC9 11 TYR B1541 THR B1557 HIS B1560 ASP B1562 SITE 2 AC9 11 ASN B1568 TRP B1614 HIS B1689 LYS B1699 SITE 3 AC9 11 MN B1805 HOH B1905 HOH B1910 SITE 1 AD1 4 HIS B1560 ASP B1562 JX8 B1804 HOH B1905 CRYST1 56.929 93.754 90.494 90.00 107.29 90.00 P 1 21 1 4 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 0.017566 0.000000 0.005468 0.00000 SCALE2 0.000000 0.010666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011574 0.00000