PDB Short entry for 4C8D HEADER OXIDOREDUCTASE 30-SEP-13 4C8D TITLE CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE 3 LYSINE-SPECIFIC TITLE 2 DEMETHYLASE 3B (KDM3B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 3B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, RESIDUES 1380-1720; COMPND 5 SYNONYM: JMJC DOMAIN OF HUMAN HISTONE 3 LYSINE-SPECIFIC DEMETHYLASE 3 COMPND 6 JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 2B, JUMONJI COMPND 7 DOMAIN-CONTAINING PROTEIN 1B, NUCLEAR PROTEIN 5QNCA; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-CTHF KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.VOLLMAR,C.JOHANSSON,C.GILEADI,S.GOUBIN,A.SZYKOWSKA,T.KROJER, AUTHOR 2 L.CRAWLEY,F.VON DELFT,C.H.ARROWSMITH,C.BOUNTRA,A.EDWARDS,U.OPPERMANN REVDAT 4 20-DEC-23 4C8D 1 REMARK LINK REVDAT 3 24-JAN-18 4C8D 1 JRNL REVDAT 2 11-DEC-13 4C8D 1 JRNL REVDAT 1 16-OCT-13 4C8D 0 JRNL AUTH M.VOLLMAR,C.JOHANSSON,C.GILEADI,S.GOUBIN,A.SZYKOWSKA, JRNL AUTH 2 T.KROJER,L.CRAWLEY,F.VON DELFT,C.H.ARROWSMITH,C.BOUNTRA, JRNL AUTH 3 A.EDWARDS,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE 3 JRNL TITL 2 LYSINE-SPECIFIC DEMETHYLASE 3B (KDM3B) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 20691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1110 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1336 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2558 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.26000 REMARK 3 B22 (A**2) : -5.38000 REMARK 3 B33 (A**2) : 8.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.780 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2644 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2417 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3592 ; 1.165 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5527 ; 0.745 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.960 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;34.052 ;23.782 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;14.558 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;11.543 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 390 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3027 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 620 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1327 ; 4.025 ; 7.818 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1324 ; 3.998 ; 7.801 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1651 ; 5.426 ;14.588 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1317 ; 4.750 ; 8.355 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1380 A 1720 REMARK 3 ORIGIN FOR THE GROUP (A): 16.5532 23.4431 135.3460 REMARK 3 T TENSOR REMARK 3 T11: 0.1643 T22: 0.1748 REMARK 3 T33: 0.3299 T12: 0.0458 REMARK 3 T13: 0.0068 T23: 0.0441 REMARK 3 L TENSOR REMARK 3 L11: 0.7074 L22: 2.6259 REMARK 3 L33: 0.2035 L12: -0.6412 REMARK 3 L13: -0.2696 L23: 0.1583 REMARK 3 S TENSOR REMARK 3 S11: 0.3013 S12: 0.2411 S13: 0.0261 REMARK 3 S21: -0.1465 S22: -0.3183 S23: -0.3256 REMARK 3 S31: -0.0646 S32: -0.1779 S33: 0.0171 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4C8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1290058540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22231 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 69.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2YPD REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.5, 0.1M AMMONIUM REMARK 280 ACETATE, 27% PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.67000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.80500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.56500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.67000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.80500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.56500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.67000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.80500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.56500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.67000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.80500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.56500 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 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 MET A 1379 REMARK 465 VAL A 1532 REMARK 465 ARG A 1533 REMARK 465 PRO A 1534 REMARK 465 ASP A 1535 REMARK 465 LEU A 1536 REMARK 465 GLY A 1537 REMARK 465 GLU A 1639 REMARK 465 ASN A 1640 REMARK 465 PRO A 1641 REMARK 465 ALA A 1721 REMARK 465 GLY A 1722 REMARK 465 ASN A 1723 REMARK 465 LEU A 1724 REMARK 465 TYR A 1725 REMARK 465 PHE A 1726 REMARK 465 GLN A 1727 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 CG CD CE NZ REMARK 470 LYS A1430 NZ REMARK 470 GLN A1436 CG CD OE1 NE2 REMARK 470 ASP A1440 CG OD1 OD2 REMARK 470 SER A1455 OG REMARK 470 ASP A1456 CG OD1 OD2 REMARK 470 VAL A1457 CG1 CG2 REMARK 470 GLU A1476 CG CD OE1 OE2 REMARK 470 LYS A1486 CG CD CE NZ REMARK 470 ASP A1487 CG OD1 OD2 REMARK 470 GLU A1492 CG CD OE1 OE2 REMARK 470 ARG A1495 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1503 CG CD OE1 OE2 REMARK 470 GLU A1507 CG CD OE1 OE2 REMARK 470 ARG A1517 CG CD NE CZ NH1 NH2 REMARK 470 ASP A1518 CG OD1 OD2 REMARK 470 SER A1525 OG REMARK 470 SER A1529 OG REMARK 470 TYR A1530 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A1531 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A1539 CG CD CE NZ REMARK 470 GLU A1550 CG CD OE1 OE2 REMARK 470 LYS A1588 CG CD CE NZ REMARK 470 GLU A1597 CG CD OE1 OE2 REMARK 470 ASP A1605 CG OD1 OD2 REMARK 470 LYS A1607 CE NZ REMARK 470 LYS A1624 CE NZ REMARK 470 GLU A1627 CG CD OE1 OE2 REMARK 470 LYS A1631 CG CD CE NZ REMARK 470 GLU A1634 CG CD OE1 OE2 REMARK 470 GLN A1636 CG CD OE1 NE2 REMARK 470 GLN A1638 CG CD OE1 NE2 REMARK 470 ASP A1643 CG OD1 OD2 REMARK 470 ASP A1649 CG OD1 OD2 REMARK 470 LYS A1660 CG CD CE NZ REMARK 470 LYS A1711 CE NZ REMARK 470 ARG A1715 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1719 CG CD OE1 OE2 REMARK 470 PHE A1720 CG CD1 CD2 CE1 CE2 CZ 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 SER A1529 38.06 -72.18 REMARK 500 GLN A1636 24.75 -142.72 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 A2721 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1560 NE2 REMARK 620 2 ASP A1562 OD2 88.5 REMARK 620 3 HIS A1689 NE2 94.9 98.9 REMARK 620 4 HOH A2043 O 81.4 74.9 172.8 REMARK 620 5 OGA A2722 O2 163.5 96.8 99.8 84.8 REMARK 620 6 OGA A2722 O2' 98.2 157.8 101.6 85.1 71.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2721 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 2722 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2723 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2724 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2725 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2726 REMARK 999 REMARK 999 SEQUENCE REMARK 999 M AT START AND AGNLYFQ AT END DUE TO CONSTRUCT DESIGN DBREF 4C8D A 1380 1720 UNP Q7LBC6 KDM3B_HUMAN 1380 1720 SEQADV 4C8D MET A 1379 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D ALA A 1721 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D GLY A 1722 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D ASN A 1723 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D LEU A 1724 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D TYR A 1725 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D PHE A 1726 UNP Q7LBC6 EXPRESSION TAG SEQADV 4C8D GLN A 1727 UNP Q7LBC6 EXPRESSION TAG SEQRES 1 A 349 MET THR SER HIS SER TRP LEU CYS ASP GLY ARG LEU LEU SEQRES 2 A 349 CYS LEU HIS ASP PRO SER ASN LYS ASN ASN TRP LYS ILE SEQRES 3 A 349 PHE ARG GLU CYS TRP LYS GLN GLY GLN PRO VAL LEU VAL SEQRES 4 A 349 SER GLY VAL HIS LYS LYS LEU LYS SER GLU LEU TRP LYS SEQRES 5 A 349 PRO GLU ALA PHE SER GLN GLU PHE GLY ASP GLN ASP VAL SEQRES 6 A 349 ASP LEU VAL ASN CYS ARG ASN CYS ALA ILE ILE SER ASP SEQRES 7 A 349 VAL LYS VAL ARG ASP PHE TRP ASP GLY PHE GLU ILE ILE SEQRES 8 A 349 CYS LYS ARG LEU ARG SER GLU ASP GLY GLN PRO MET VAL SEQRES 9 A 349 LEU LYS LEU LYS ASP TRP PRO PRO GLY GLU ASP PHE ARG SEQRES 10 A 349 ASP MET MET PRO THR ARG PHE GLU ASP LEU MET GLU ASN SEQRES 11 A 349 LEU PRO LEU PRO GLU TYR THR LYS ARG ASP GLY ARG LEU SEQRES 12 A 349 ASN LEU ALA SER ARG LEU PRO SER TYR PHE VAL ARG PRO SEQRES 13 A 349 ASP LEU GLY PRO LYS MET TYR ASN ALA TYR GLY LEU ILE SEQRES 14 A 349 THR ALA GLU ASP ARG ARG VAL GLY THR THR ASN LEU HIS SEQRES 15 A 349 LEU ASP VAL SER ASP ALA VAL ASN VAL MET VAL TYR VAL SEQRES 16 A 349 GLY ILE PRO ILE GLY GLU GLY ALA HIS ASP GLU GLU VAL SEQRES 17 A 349 LEU LYS THR ILE ASP GLU GLY ASP ALA ASP GLU VAL THR SEQRES 18 A 349 LYS GLN ARG ILE HIS ASP GLY LYS GLU LYS PRO GLY ALA SEQRES 19 A 349 LEU TRP HIS ILE TYR ALA ALA LYS ASP ALA GLU LYS ILE SEQRES 20 A 349 ARG GLU LEU LEU ARG LYS VAL GLY GLU GLU GLN GLY GLN SEQRES 21 A 349 GLU ASN PRO PRO ASP HIS ASP PRO ILE HIS ASP GLN SER SEQRES 22 A 349 TRP TYR LEU ASP GLN THR LEU ARG LYS ARG LEU TYR GLU SEQRES 23 A 349 GLU TYR GLY VAL GLN GLY TRP ALA ILE VAL GLN PHE LEU SEQRES 24 A 349 GLY ASP ALA VAL PHE ILE PRO ALA GLY ALA PRO HIS GLN SEQRES 25 A 349 VAL HIS ASN LEU TYR SER CYS ILE LYS VAL ALA GLU ASP SEQRES 26 A 349 PHE VAL SER PRO GLU HIS VAL LYS HIS CYS PHE ARG LEU SEQRES 27 A 349 THR GLN GLU PHE ALA GLY ASN LEU TYR PHE GLN HET MN A2721 1 HET OGA A2722 10 HET GOL A2723 6 HET ACT A2724 4 HET ACT A2725 4 HET CL A2726 1 HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN MN 2+ FORMUL 3 OGA C4 H5 N O5 FORMUL 4 GOL C3 H8 O3 FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 7 CL CL 1- FORMUL 8 HOH *69(H2 O) HELIX 1 1 ASN A 1400 GLN A 1411 1 12 HELIX 2 2 GLY A 1419 LEU A 1424 5 6 HELIX 3 3 LYS A 1425 TRP A 1429 5 5 HELIX 4 4 LYS A 1430 GLY A 1439 1 10 HELIX 5 5 VAL A 1459 GLY A 1465 1 7 HELIX 6 6 ILE A 1469 ARG A 1472 5 4 HELIX 7 7 GLU A 1492 MET A 1498 1 7 HELIX 8 8 MET A 1498 LEU A 1509 1 12 HELIX 9 9 LEU A 1511 LYS A 1516 1 6 HELIX 10 10 ALA A 1549 VAL A 1554 5 6 HELIX 11 11 HIS A 1582 GLY A 1593 1 12 HELIX 12 12 ASP A 1596 ASP A 1605 1 10 HELIX 13 13 ALA A 1618 LYS A 1620 5 3 HELIX 14 14 ASP A 1621 GLU A 1635 1 15 HELIX 15 15 ASP A 1645 GLN A 1650 1 6 HELIX 16 16 ASP A 1655 GLY A 1667 1 13 HELIX 17 17 SER A 1706 GLU A 1708 5 3 HELIX 18 18 HIS A 1709 PHE A 1720 1 12 SHEET 1 AA 7 HIS A1382 LEU A1385 0 SHEET 2 AA 7 LEU A1390 LEU A1393 -1 O LEU A1390 N LEU A1385 SHEET 3 AA 7 VAL A1415 VAL A1417 1 O LEU A1416 N LEU A1393 SHEET 4 AA 7 ALA A1680 ILE A1683 -1 O ALA A1680 N VAL A1417 SHEET 5 AA 7 ASP A1565 GLY A1574 -1 O ALA A1566 N ILE A1683 SHEET 6 AA 7 SER A1696 PHE A1704 -1 O SER A1696 N GLY A1574 SHEET 7 AA 7 LYS A1539 ALA A1543 -1 O LYS A1539 N ALA A1701 SHEET 1 AB 3 ILE A1453 LYS A1458 0 SHEET 2 AB 3 ASP A1442 ASN A1447 -1 O VAL A1443 N VAL A1457 SHEET 3 AB 3 LEU A1483 LEU A1485 -1 O LYS A1484 N VAL A1446 SHEET 1 AC 4 THR A1557 HIS A1560 0 SHEET 2 AC 4 HIS A1689 ASN A1693 -1 O HIS A1689 N HIS A1560 SHEET 3 AC 4 PRO A1610 ILE A1616 -1 O LEU A1613 N HIS A1692 SHEET 4 AC 4 TRP A1671 PHE A1676 -1 O TRP A1671 N ILE A1616 LINK NE2 HIS A1560 MN MN A2721 1555 1555 2.23 LINK OD2 ASP A1562 MN MN A2721 1555 1555 2.26 LINK NE2 HIS A1689 MN MN A2721 1555 1555 2.01 LINK O HOH A2043 MN MN A2721 1555 1555 1.72 LINK MN MN A2721 O2 OGA A2722 1555 1555 2.12 LINK MN MN A2721 O2' OGA A2722 1555 1555 2.30 CISPEP 1 TRP A 1488 PRO A 1489 0 -9.95 SITE 1 AC1 5 HIS A1560 ASP A1562 HIS A1689 HOH A2043 SITE 2 AC1 5 OGA A2722 SITE 1 AC2 15 TYR A1541 THR A1557 HIS A1560 ASP A1562 SITE 2 AC2 15 ASN A1568 TRP A1614 ILE A1683 HIS A1689 SITE 3 AC2 15 VAL A1691 LYS A1699 HOH A2043 HOH A2048 SITE 4 AC2 15 HOH A2065 HOH A2068 MN A2721 SITE 1 AC3 7 TRP A1402 LYS A1403 ARG A1406 GLU A1407 SITE 2 AC3 7 GLY A1580 ALA A1581 HOH A2069 SITE 1 AC4 3 TRP A1384 GLY A1388 GLN A1413 SITE 1 AC5 5 ARG A1449 ARG A1472 VAL A1482 GLY A1545 SITE 2 AC5 5 GLU A1579 SITE 1 AC6 3 LEU A1511 GLU A1513 HOH A2001 CRYST1 83.340 85.610 117.130 90.00 90.00 90.00 I 2 2 2 8 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 0.011999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008538 0.00000