HEADER OXIDOREDUCTASE 02-JUN-15 5A3T TITLE CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH TITLE 2 KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2- TITLE 3 OXOETHYL)AMINO)METHYL) ISONICOTINIC ACID). COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, RESIDUES 26-101,374-772; COMPND 5 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE COMPND 6 JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, COMPND 7 RETINOBLASTOMA -BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1; 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: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, LYSINE-SPECIFIC DEMETHYLASE 5B EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,C.JOHANSSON,C.GILEADI,J.KOPEC,C.STRAIN-DAMERELL, AUTHOR 2 K.KUPINSKA,N.A.BURGESSBROWN,F.VON DELFT,C.H.ARROWSMITH,C.BOUNTRA, AUTHOR 3 A.M.EDWARDS,U.OPPERMANN REVDAT 4 29-JUN-16 5A3T 1 JRNL REVDAT 3 01-JUN-16 5A3T 1 JRNL REVDAT 2 25-MAY-16 5A3T 1 JRNL REVDAT 1 17-JUN-15 5A3T 0 JRNL AUTH C.JOHANSSON,S.VELUPILLAI,A.TUMBER,A.SZYKOWSKA,E.S.HOOKWAY, JRNL AUTH 2 R.P.NOWAK,C.STRAIN-DAMERELL,C.GILEADI,M.PHILPOTT, JRNL AUTH 3 N.BURGESS-BROWN,N.WU,J.KOPEC,A.NUZZI,H.STEUBER,U.EGNER, JRNL AUTH 4 V.BADOCK,S.MUNRO,N.B.LATHANGUE,S.WESTAWAY,J.BROWN, JRNL AUTH 5 N.ATHANASOU,R.PRINJHA,P.E.BRENNAN,U.OPPERMANN JRNL TITL STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE JRNL TITL 2 DEMETHYLASE INHIBITOR DEVELOPMENT. JRNL REF NAT.CHEM.BIOL. V. 12 539 2016 JRNL REFN ISSN 1552-4450 JRNL PMID 27214403 JRNL DOI 10.1038/NCHEMBIO.2087 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 122.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.96 REMARK 3 NUMBER OF REFLECTIONS : 67433 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) : 0.20046 REMARK 3 R VALUE (WORKING SET) : 0.19944 REMARK 3 FREE R VALUE : 0.22039 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 3534 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) : 1.900 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.949 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4893 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.317 REMARK 3 BIN FREE R VALUE SET COUNT : 272 REMARK 3 BIN FREE R VALUE : 0.315 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.632 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27 REMARK 3 B22 (A**2) : 0.27 REMARK 3 B33 (A**2) : -0.86 REMARK 3 B12 (A**2) : 0.13 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.817 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3866 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3601 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5238 ; 1.497 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8321 ; 1.009 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 6.043 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;35.217 ;23.722 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 639 ;12.448 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.976 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4265 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 0.002 ; 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): 1826 ; 2.268 ; 3.723 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1822 ; 2.268 ; 3.723 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2279 ; 3.559 ; 5.563 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2038 ; 2.770 ; 4.083 REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : NULL 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 5A3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-15. REMARK 100 THE PDBE ID CODE IS EBI-63930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 0.917410 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71027 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90 REMARK 200 RESOLUTION RANGE LOW (A) : 47.71 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 22.3 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.5 REMARK 200 R MERGE FOR SHELL (I) : 1.50 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4-AUTOMR REMARK 200 STARTING MODEL: PDB ENTRY 51AF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.7 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 0.8M REMARK 280 POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE REMARK 280 MONOBASIC 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 101.00600 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 50.50300 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 75.75450 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 25.25150 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 126.25750 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 101.00600 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 50.50300 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 25.25150 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 75.75450 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 126.25750 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 LEU A 101 REMARK 465 GLY A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 104 REMARK 465 GLY A 105 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 REMARK 465 SER A 754 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 LYS A 100 CG CD CE NZ REMARK 470 GLN A 545 CG CD OE1 NE2 REMARK 470 HIS A 550 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE B ARG A 679 NH2B ARG A 679 10665 2.04 REMARK 500 CZ B ARG A 679 CZ B ARG A 679 10665 1.37 REMARK 500 CZ B ARG A 679 NH1B ARG A 679 10665 2.09 REMARK 500 CZ B ARG A 679 NH2B ARG A 679 10665 1.10 REMARK 500 NH1B ARG A 679 NH2B ARG A 679 10665 2.16 REMARK 500 NH2B ARG A 679 NH2B ARG A 679 10665 0.40 REMARK 500 O HOH A 2079 O HOH A 2079 9765 1.40 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 CYS A 76 -67.93 -152.36 REMARK 500 ASP A 77 132.11 114.11 REMARK 500 ILE A 479 41.40 38.86 REMARK 500 PHE A 493 -7.05 78.33 REMARK 500 PHE A 700 -56.72 -149.98 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 A1765 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 MMK A1756 NAR 94.1 REMARK 620 3 MMK A1756 N 82.8 71.8 REMARK 620 4 GLU A 501 OE2 98.1 165.7 102.3 REMARK 620 5 HIS A 587 NE2 82.9 109.0 165.7 80.1 REMARK 620 6 HOH A2124 O 175.7 82.9 99.0 85.3 95.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1754 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 692 SG REMARK 620 2 CYS A 715 SG 119.5 REMARK 620 3 HIS A 718 ND1 114.8 96.1 REMARK 620 4 CYS A 695 SG 106.0 112.1 107.9 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 A1754 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MMK A1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1757 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1758 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1760 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1761 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1763 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1764 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1765 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A3N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX REMARK 900 WITH KDOAM25A REMARK 900 RELATED ID: 5A3W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX REMARK 900 WITH PYRIDINE-2,6-DICARBOXYLIC ACID (PDCA) REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE REMARK 999 L101 TO G369 WAS DELETED AND LINKED BY FOUR GLYCINE REMARK 999 RESIDUES (GLYCINE LINKER). DBREF 5A3T A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5A3T A 374 772 UNP Q9UGL1 KDM5B_HUMAN 374 772 SEQADV 5A3T SER A -1 UNP Q9UGL1 EXPRESSION TAG SEQADV 5A3T MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQADV 5A3T GLY A 102 UNP Q9UGL1 LINKER SEQADV 5A3T GLY A 103 UNP Q9UGL1 LINKER SEQADV 5A3T GLY A 104 UNP Q9UGL1 LINKER SEQADV 5A3T GLY A 105 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 A1754 1 HET EPE A1755 15 HET MMK A1756 22 HET NI A1757 1 HET EDO A1758 4 HET EDO A1759 4 HET EDO A1760 4 HET EDO A1761 4 HET EDO A1762 4 HET EDO A1763 4 HET EDO A1764 4 HET MN A1765 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE HETNAM 2 EPE ETHANESULFONIC ACID HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION HETNAM MMK 2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL) HETNAM 2 MMK AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4- HETNAM 3 MMK CARBOXYLIC ACID HETNAM NI NICKEL (II) ION HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 2 EDO 7(C2 H6 O2) FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 MN MN 2+ FORMUL 5 ZN ZN 2+ FORMUL 6 MMK C15 H22 N4 O3 FORMUL 7 NI NI 2+ FORMUL 8 HOH *242(H2 O) HELIX 1 1 SER A 38 ASP A 44 1 7 HELIX 2 2 ASP A 44 GLU A 57 1 14 HELIX 3 3 LEU A 379 ASN A 395 1 17 HELIX 4 4 PRO A 397 VAL A 401 5 5 HELIX 5 5 PRO A 402 THR A 416 1 15 HELIX 6 6 SER A 431 GLY A 435 1 5 HELIX 7 7 SER A 448 GLU A 453 1 6 HELIX 8 8 ASN A 463 MET A 467 5 5 HELIX 9 9 ASP A 478 MET A 482 5 5 HELIX 10 10 GLU A 501 SER A 505 5 5 HELIX 11 11 PRO A 523 TYR A 525 5 3 HELIX 12 12 ALA A 526 ALA A 538 1 13 HELIX 13 13 PRO A 539 VAL A 543 5 5 HELIX 14 14 ASP A 547 HIS A 550 5 4 HELIX 15 15 ASN A 557 HIS A 564 1 8 HELIX 16 16 TRP A 607 HIS A 622 1 16 HELIX 17 17 SER A 628 SER A 638 1 11 HELIX 18 18 LYS A 639 LEU A 643 5 5 HELIX 19 19 ASP A 644 LEU A 672 1 29 HELIX 20 20 ASP A 681 LEU A 685 5 5 HELIX 21 21 PRO A 686 ARG A 690 5 5 HELIX 22 22 HIS A 718 LEU A 722 5 5 HELIX 23 23 PRO A 726 TYR A 728 5 3 HELIX 24 24 THR A 737 GLU A 753 1 17 SHEET 1 AA 8 VAL A 34 PHE A 35 0 SHEET 2 AA 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35 SHEET 3 AA 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64 SHEET 4 AA 8 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581 SHEET 5 AA 8 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512 SHEET 6 AA 8 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599 SHEET 7 AA 8 THR A 422 ALA A 430 -1 O GLY A 426 N VAL A 489 SHEET 8 AA 8 ARG A 86 ARG A 89 -1 O ARG A 86 N TYR A 425 SHEET 1 AB 2 HIS A 82 PHE A 83 0 SHEET 2 AB 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83 SHEET 1 AC 2 GLN A 96 THR A 97 0 SHEET 2 AC 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96 SHEET 1 AD 4 SER A 495 HIS A 499 0 SHEET 2 AD 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499 SHEET 3 AD 4 LYS A 517 GLY A 521 -1 O THR A 518 N PHE A 590 SHEET 4 AD 4 TYR A 569 GLN A 573 -1 O TYR A 569 N GLY A 521 SHEET 1 AE 3 ASP A 676 ARG A 679 0 SHEET 2 AE 3 TYR A 730 TYR A 734 1 O TYR A 730 N ASP A 676 SHEET 3 AE 3 SER A 702 CYS A 706 -1 O ALA A 703 N ARG A 733 SSBOND 1 CYS A 706 CYS A 723 1555 1555 2.08 SSBOND 2 CYS A 708 CYS A 725 1555 1555 2.03 LINK ZN ZN A1754 SG CYS A 692 1555 1555 2.03 LINK ZN ZN A1754 SG CYS A 695 1555 1555 2.41 LINK ZN ZN A1754 ND1 HIS A 718 1555 1555 2.24 LINK ZN ZN A1754 SG CYS A 715 1555 1555 2.22 LINK MN MN A1765 NE2 HIS A 587 1555 1555 2.28 LINK MN MN A1765 O HOH A2124 1555 1555 2.28 LINK MN MN A1765 OE2 GLU A 501 1555 1555 2.02 LINK MN MN A1765 N MMK A1756 1555 1555 2.23 LINK MN MN A1765 NAR MMK A1756 1555 1555 2.07 LINK MN MN A1765 NE2 HIS A 499 1555 1555 2.19 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 16 ILE A 500 TRP A 504 LEU A 541 PHE A 542 SITE 2 AC2 16 LEU A 552 VAL A 553 ARG A 584 TYR A 586 SITE 3 AC2 16 HIS A 617 TYR A 618 LEU A 621 ARG A 623 SITE 4 AC2 16 HOH A2117 HOH A2123 HOH A2150 HOH A2241 SITE 1 AC3 17 ARG A 98 TYR A 425 ASP A 428 TYR A 488 SITE 2 AC3 17 PHE A 496 HIS A 499 GLU A 501 LYS A 517 SITE 3 AC3 17 TRP A 519 HIS A 587 VAL A 600 ASN A 601 SITE 4 AC3 17 MN A1765 HOH A2051 HOH A2124 HOH A2129 SITE 5 AC3 17 HOH A2242 SITE 1 AC4 2 HIS A 622 HIS A 718 SITE 1 AC5 6 ASP A 630 CYS A 699 PHE A 700 MET A 701 SITE 2 AC5 6 SER A 702 HOH A2184 SITE 1 AC6 3 ARG A 666 THR A 737 HOH A2234 SITE 1 AC7 8 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC7 8 GLU A 419 ASP A 420 VAL A 421 HOH A2087 SITE 1 AC8 5 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 2 AC8 5 HOH A2168 SITE 1 AC9 7 PRO A 465 SER A 470 LEU A 472 MET A 482 SITE 2 AC9 7 ASN A 601 PHE A 602 CYS A 603 SITE 1 BC1 10 GLU A 468 SER A 470 VAL A 471 LEU A 472 SITE 2 BC1 10 ALA A 473 HIS A 474 MET A 636 LEU A 643 SITE 3 BC1 10 VAL A 647 HOH A2103 SITE 1 BC2 7 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 BC2 7 VAL A 693 LEU A 712 LEU A 713 SITE 1 BC3 5 HIS A 499 GLU A 501 HIS A 587 MMK A1756 SITE 2 BC3 5 HOH A2124 CRYST1 141.852 141.852 151.509 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 0.007050 0.004070 0.000000 0.00000 SCALE2 0.000000 0.008140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006600 0.00000