HEADER OXIDOREDUCTASE 29-APR-15 5A1F TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PLU1 IN COMPLEX WITH N- TITLE 2 OXALYLGLYCINE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE COMPND 3 5B; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: JMJC DOMAIN, RESIDUES, JMJC DOMAIN, RESIDUES; COMPND 6 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, COMPND 7 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA- COMPND 8 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1, CANCER/TESTIS ANTIGEN 31, CT31, COMPND 9 HISTONE DEMETHYLASE JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN COMPND 10 1B, PLU-1, RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1; COMPND 11 EC: 1.14.11.-, 1.14.11.-; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM5B, JARID1B, PLU1, RBBP2H1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, LYSINE-SPECIFIC DEMETHYLASE 5B EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,C.JOHANSSON,C.STRAIN-DAMERELL,C.GILEADI,A.SZYKOWSKA, AUTHOR 2 K.KUPINSKA,J.KOPEC,T.KROJER,H.STEUBER,F.VON DELFT,N.A.BURGESS-BROWN, AUTHOR 3 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN REVDAT 7 10-JAN-24 5A1F 1 REMARK LINK REVDAT 6 29-JUN-16 5A1F 1 JRNL REVDAT 5 01-JUN-16 5A1F 1 JRNL REVDAT 4 25-MAY-16 5A1F 1 JRNL REVDAT 3 20-MAY-15 5A1F 1 SOURCE REMARK REVDAT 2 13-MAY-15 5A1F 1 TITLE AUTHOR REVDAT 1 06-MAY-15 5A1F 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 50341 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2629 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3678 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3603 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -1.32000 REMARK 3 B12 (A**2) : 0.20000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.166 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3797 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3488 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5155 ; 1.503 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8048 ; 0.985 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 6.391 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;35.102 ;23.523 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 608 ;15.113 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.544 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4224 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 881 ; 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): 1808 ; 3.070 ; 4.569 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1807 ; 3.064 ; 4.567 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2258 ; 4.623 ; 6.833 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1988 ; 3.638 ; 4.945 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 : 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 RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY SOME SIDE CHAINS REMARK 3 REMOVED AND SOME OF THE RESIDUES HAVE ALTERNATIVE CONFIRMATION. REMARK 4 REMARK 4 5A1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-15. REMARK 100 THE DEPOSITION ID IS D_1290063710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 287 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91742 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52970 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : 0.09000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4I REMARK 200 STARTING MODEL: PDB ENTRY 4GIO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 0.8M POTASSIUM REMARK 280 PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE 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 101.41933 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 50.70967 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.06450 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 25.35483 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 126.77417 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 101.41933 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 50.70967 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 25.35483 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 76.06450 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 126.77417 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 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 LYS A 100 REMARK 465 LEU A 101 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 REMARK 465 ILE A 445 REMARK 465 LYS A 446 REMARK 465 LEU A 447 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 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 LEU A 81 CG CD1 CD2 REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 99 CG1 CG2 REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 PHE A 434 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 442 CG OD1 OD2 REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 GLN A 545 CG CD OE1 NE2 REMARK 470 LYS A 653 CE NZ REMARK 470 LYS A 720 CG CD CE NZ REMARK 470 LYS A 749 CE NZ 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 OE1 GLU A 515 O2 EDO A 1764 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 584 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TRP A 70 97.09 -68.02 REMARK 500 LEU A 93 -3.19 60.77 REMARK 500 PHE A 434 -72.85 -83.70 REMARK 500 PHE A 493 -9.20 77.55 REMARK 500 ALA A 538 68.63 -152.68 REMARK 500 HIS A 550 32.55 -141.46 REMARK 500 PHE A 700 -54.96 -149.09 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 A1757 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 91 OD1 REMARK 620 2 THR A 416 O 114.7 REMARK 620 3 GLU A 419 O 104.2 66.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1758 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 100.0 REMARK 620 3 HIS A 587 NE2 88.4 82.1 REMARK 620 4 OGA A1756 O2' 88.5 170.9 101.5 REMARK 620 5 OGA A1756 O1 167.7 92.2 93.1 79.3 REMARK 620 6 HOH A2098 O 88.7 93.0 173.7 84.0 91.0 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 695 SG 106.9 REMARK 620 3 CYS A 715 SG 117.1 112.5 REMARK 620 4 HIS A 718 ND1 113.4 109.0 97.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1755 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 706 SG REMARK 620 2 CYS A 708 SG 115.6 REMARK 620 3 CYS A 723 SG 111.5 107.2 REMARK 620 4 CYS A 725 SG 103.3 111.8 107.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1754 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1757 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1758 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1760 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1761 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1763 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1764 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1765 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1766 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1767 DBREF 5A1F A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5A1F A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770 SEQADV 5A1F SER A -1 UNP Q9UGL1 EXPRESSION TAG SEQADV 5A1F MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQRES 1 A 475 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 475 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 475 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 475 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 475 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 475 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 475 ALA ARG ASP TYR THR LEU ARG THR PHE GLY GLU MET ALA SEQRES 8 A 475 ASP ALA PHE LYS SER ASP TYR PHE ASN MET PRO VAL HIS SEQRES 9 A 475 MET VAL PRO THR GLU LEU VAL GLU LYS GLU PHE TRP ARG SEQRES 10 A 475 LEU VAL SER THR ILE GLU GLU ASP VAL THR VAL GLU TYR SEQRES 11 A 475 GLY ALA ASP ILE ALA SER LYS GLU PHE GLY SER GLY PHE SEQRES 12 A 475 PRO VAL ARG ASP GLY LYS ILE LYS LEU SER PRO GLU GLU SEQRES 13 A 475 GLU GLU TYR LEU ASP SER GLY TRP ASN LEU ASN ASN MET SEQRES 14 A 475 PRO VAL MET GLU GLN SER VAL LEU ALA HIS ILE THR ALA SEQRES 15 A 475 ASP ILE CYS GLY MET LYS LEU PRO TRP LEU TYR VAL GLY SEQRES 16 A 475 MET CYS PHE SER SER PHE CYS TRP HIS ILE GLU ASP HIS SEQRES 17 A 475 TRP SER TYR SER ILE ASN TYR LEU HIS TRP GLY GLU PRO SEQRES 18 A 475 LYS THR TRP TYR GLY VAL PRO GLY TYR ALA ALA GLU GLN SEQRES 19 A 475 LEU GLU ASN VAL MET LYS LYS LEU ALA PRO GLU LEU PHE SEQRES 20 A 475 VAL SER GLN PRO ASP LEU LEU HIS GLN LEU VAL THR ILE SEQRES 21 A 475 MET ASN PRO ASN THR LEU MET THR HIS GLU VAL PRO VAL SEQRES 22 A 475 TYR ARG THR ASN GLN CYS ALA GLY GLU PHE VAL ILE THR SEQRES 23 A 475 PHE PRO ARG ALA TYR HIS SER GLY PHE ASN GLN GLY PHE SEQRES 24 A 475 ASN PHE ALA GLU ALA VAL ASN PHE CYS THR VAL ASP TRP SEQRES 25 A 475 LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS TYR ARG LEU SEQRES 26 A 475 LEU HIS ARG TYR CYS VAL PHE SER HIS ASP GLU MET ILE SEQRES 27 A 475 CYS LYS MET ALA SER LYS ALA ASP VAL LEU ASP VAL VAL SEQRES 28 A 475 VAL ALA SER THR VAL GLN LYS ASP MET ALA ILE MET ILE SEQRES 29 A 475 GLU ASP GLU LYS ALA LEU ARG GLU THR VAL ARG LYS LEU SEQRES 30 A 475 GLY VAL ILE ASP SER GLU ARG MET ASP PHE GLU LEU LEU SEQRES 31 A 475 PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS LYS THR THR SEQRES 32 A 475 CYS PHE MET SER ALA ILE SER CYS SER CYS LYS PRO GLY SEQRES 33 A 475 LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU LEU CYS SER SEQRES 34 A 475 CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR ARG TYR THR SEQRES 35 A 475 LEU ASP ASP LEU TYR PRO MET MET ASN ALA LEU LYS LEU SEQRES 36 A 475 ARG ALA GLU SER TYR ASN GLU TRP ALA LEU ASN VAL ASN SEQRES 37 A 475 GLU ALA LEU GLU ALA LYS ILE HET ZN A1754 1 HET ZN A1755 1 HET OGA A1756 10 HET MN A1757 1 HET MN A1758 1 HET PO4 A1759 5 HET EPE A1760 15 HET EDO A1761 4 HET EDO A1762 4 HET EDO A1763 4 HET EDO A1764 4 HET EDO A1765 4 HET EDO A1766 4 HET EDO A1767 4 HETNAM ZN ZINC ION HETNAM OGA N-OXALYLGLYCINE HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 OGA C4 H5 N O5 FORMUL 5 MN 2(MN 2+) FORMUL 7 PO4 O4 P 3- FORMUL 8 EPE C8 H18 N2 O4 S FORMUL 9 EDO 7(C2 H6 O2) FORMUL 16 HOH *204(H2 O) HELIX 1 1 SER A 38 ALA A 43 1 6 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 448 SER A 457 1 10 HELIX 7 7 ASN A 462 MET A 467 1 6 HELIX 8 8 SER A 470 ILE A 475 5 6 HELIX 9 9 ILE A 479 LEU A 484 1 6 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 ILE A 429 -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 LINK OD1 ASN A 91 MN MN A1757 1555 1555 2.62 LINK O THR A 416 MN MN A1757 1555 1555 2.76 LINK O GLU A 419 MN MN A1757 1555 1555 2.76 LINK NE2 HIS A 499 MN MN A1758 1555 1555 2.22 LINK OE2 GLU A 501 MN MN A1758 1555 1555 2.06 LINK NE2 HIS A 587 MN MN A1758 1555 1555 2.17 LINK SG CYS A 692 ZN ZN A1754 1555 1555 2.22 LINK SG CYS A 695 ZN ZN A1754 1555 1555 2.41 LINK SG CYS A 706 ZN ZN A1755 1555 1555 2.31 LINK SG CYS A 708 ZN ZN A1755 1555 1555 2.27 LINK SG CYS A 715 ZN ZN A1754 1555 1555 2.23 LINK ND1 HIS A 718 ZN ZN A1754 1555 1555 2.19 LINK SG CYS A 723 ZN ZN A1755 1555 1555 2.36 LINK SG CYS A 725 ZN ZN A1755 1555 1555 2.53 LINK O2' OGA A1756 MN MN A1758 1555 1555 2.06 LINK O1 OGA A1756 MN MN A1758 1555 1555 2.20 LINK MN MN A1758 O HOH A2098 1555 1555 1.90 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 4 CYS A 706 CYS A 708 CYS A 723 CYS A 725 SITE 1 AC3 14 PHE A 496 HIS A 499 GLU A 501 SER A 507 SITE 2 AC3 14 ASN A 509 LYS A 517 TRP A 519 HIS A 587 SITE 3 AC3 14 ALA A 599 MN A1758 EDO A1765 EDO A1766 SITE 4 AC3 14 HOH A2098 HOH A2203 SITE 1 AC4 5 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC4 5 GLU A 419 SITE 1 AC5 5 HIS A 499 GLU A 501 HIS A 587 OGA A1756 SITE 2 AC5 5 HOH A2098 SITE 1 AC6 4 HIS A 622 LYS A 694 HIS A 718 HOH A2143 SITE 1 AC7 16 ILE A 500 TRP A 504 GLU A 531 MET A 534 SITE 2 AC7 16 LEU A 541 LEU A 552 VAL A 553 ARG A 584 SITE 3 AC7 16 TYR A 586 HIS A 617 TYR A 618 LEU A 621 SITE 4 AC7 16 ARG A 623 HOH A2096 HOH A2101 HOH A2149 SITE 1 AC8 7 ILE A 475 ALA A 477 PHE A 627 SER A 628 SITE 2 AC8 7 GLU A 631 MET A 632 HOH A2184 SITE 1 AC9 9 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AC9 9 VAL A 693 GLY A 711 LEU A 712 LEU A 713 SITE 3 AC9 9 HOH A2204 SITE 1 BC1 4 VAL A 674 ILE A 675 HOH A2167 HOH A2171 SITE 1 BC2 8 ALA A 386 ASP A 387 LYS A 390 MET A 491 SITE 2 BC2 8 CYS A 492 GLU A 515 GLY A 593 PHE A 594 SITE 1 BC3 7 TYR A 425 SER A 494 SER A 495 LYS A 517 SITE 2 BC3 7 ASN A 591 OGA A1756 HOH A2203 SITE 1 BC4 6 TYR A 488 GLU A 501 ASN A 601 OGA A1756 SITE 2 BC4 6 HOH A2090 HOH A2098 SITE 1 BC5 6 ASP A 630 CYS A 699 PHE A 700 MET A 701 SITE 2 BC5 6 SER A 702 HOH A2154 CRYST1 141.855 141.855 152.129 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 0.007049 0.004070 0.000000 0.00000 SCALE2 0.000000 0.008140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006573 0.00000