HEADER OXIDOREDUCTASE 04-DEC-15 5F5A TITLE CRYSTAL STRUCTURE OF HUMAN JMJD2D COMPLEXED WITH KDOAM16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: OXIDOREDUCTASE-2OG; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D; COMPND 7 EC: 1.14.11.-; COMPND 8 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: KDM4D, JHDM3D, JMJD2D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS DOUBLE-STRANDED BETA HELIX, DEMETHYLASE, OXYGENASE, OXIDOREDUCTASE, KEYWDS 2 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR T.KROJER,M.VOLLMAR,L.CRAWLEY,A.R.BRADLEY,A.SZYKOWSKA,G.F.RUDA,H.YANG, AUTHOR 2 N.BURGESS-BROWN,P.BRENNAN,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS, AUTHOR 3 U.OPPERMANN,F.VON DELFT,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 10-JAN-24 5F5A 1 REMARK LINK REVDAT 3 14-SEP-16 5F5A 1 AUTHOR REVDAT 2 27-APR-16 5F5A 1 JRNL REVDAT 1 16-DEC-15 5F5A 0 JRNL AUTH V.BAVETSIAS,R.M.LANIGAN,G.F.RUDA,B.ATRASH,M.G.MCLAUGHLIN, JRNL AUTH 2 A.TUMBER,N.Y.MOK,Y.V.LE BIHAN,S.DEMPSTER,K.J.BOXALL, JRNL AUTH 3 F.JEGANATHAN,S.B.HATCH,P.SAVITSKY,S.VELUPILLAI,T.KROJER, JRNL AUTH 4 K.S.ENGLAND,J.SEJBERG,C.THAI,A.DONOVAN,A.PAL,G.SCOZZAFAVA, JRNL AUTH 5 J.M.BENNETT,A.KAWAMURA,C.JOHANSSON,A.SZYKOWSKA,C.GILEADI, JRNL AUTH 6 N.A.BURGESS-BROWN,F.VON DELFT,U.OPPERMANN,Z.WALTERS, JRNL AUTH 7 J.SHIPLEY,F.I.RAYNAUD,S.M.WESTAWAY,R.K.PRINJHA,O.FEDOROV, JRNL AUTH 8 R.BURKE,C.J.SCHOFIELD,I.M.WESTWOOD,C.BOUNTRA,S.MULLER, JRNL AUTH 9 R.L.VAN MONTFORT,P.E.BRENNAN,J.BLAGG JRNL TITL 8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONE DERIVATIVES JRNL TITL 2 AS POTENT, CELL PERMEABLE, KDM4 (JMJD2) AND KDM5 (JARID1) JRNL TITL 3 HISTONE LYSINE DEMETHYLASE INHIBITORS. JRNL REF J.MED.CHEM. V. 59 1388 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26741168 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01635 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 71618 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3769 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) : 1.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5183 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.1540 REMARK 3 BIN FREE R VALUE SET COUNT : 289 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 344 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : -0.62000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.502 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3001 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2735 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4076 ; 1.532 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6302 ; 0.990 ; 2.993 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 6.287 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;35.893 ;23.706 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;11.962 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;22.831 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 407 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3492 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 754 ; 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): 1425 ; 1.610 ; 1.593 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1426 ; 1.610 ; 1.594 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1816 ; 2.137 ; 2.399 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5736 ; 1.734 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 103 ;36.731 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5891 ; 9.883 ; 5.000 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 REMARK 4 REMARK 4 5F5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.92000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75484 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 50.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4D6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG3350 , 0.1M HEPES PH 7.0 , REMARK 280 0.25M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 75.18000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.64000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.77000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.64000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.59000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.64000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.77000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.64000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.59000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.18000 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 TOTAL BURIED SURFACE AREA: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 ASN A 9 REMARK 465 CYS A 10 REMARK 465 ASP A 341 REMARK 465 ARG A 342 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 94 CG CD CE NZ REMARK 470 GLU A 119 CD OE1 OE2 REMARK 470 LYS A 166 CG CD CE NZ REMARK 470 ARG A 225 NE CZ NH1 NH2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 319 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 338 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 340 CG CD OE1 NE2 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 ASN A 176 N - CA - CB ANGL. DEV. = -11.1 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 LYS A 186 -6.90 77.24 REMARK 500 MET A 196 19.84 59.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 844 DISTANCE = 6.21 ANGSTROMS 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 101.4 REMARK 620 3 HIS A 280 NE2 84.0 90.2 REMARK 620 4 5V0 A 403 N1 96.0 91.6 178.3 REMARK 620 5 5V0 A 403 N 94.8 160.9 101.7 76.6 REMARK 620 6 HOH A 529 O 166.7 88.9 87.7 92.0 76.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 HIS A 244 NE2 110.1 REMARK 620 3 CYS A 310 SG 117.5 108.6 REMARK 620 4 CYS A 312 SG 114.0 99.0 106.0 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5V0 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 420 DBREF 5F5A A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342 SEQADV 5F5A TYR A -3 UNP Q6B0I6 EXPRESSION TAG SEQADV 5F5A PHE A -2 UNP Q6B0I6 EXPRESSION TAG SEQADV 5F5A GLN A -1 UNP Q6B0I6 EXPRESSION TAG SEQADV 5F5A SER A 0 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 346 TYR PHE GLN SER MET GLU THR MET LYS SER LYS ALA ASN SEQRES 2 A 346 CYS ALA GLN ASN PRO ASN CYS ASN ILE MET ILE PHE HIS SEQRES 3 A 346 PRO THR LYS GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE SEQRES 4 A 346 ALA TYR MET GLU SER GLN GLY ALA HIS ARG ALA GLY LEU SEQRES 5 A 346 ALA LYS ILE ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU SEQRES 6 A 346 THR TYR ASP ASN ILE SER GLU ILE LEU ILE ALA THR PRO SEQRES 7 A 346 LEU GLN GLN VAL ALA SER GLY ARG ALA GLY VAL PHE THR SEQRES 8 A 346 GLN TYR HIS LYS LYS LYS LYS ALA MET THR VAL GLY GLU SEQRES 9 A 346 TYR ARG HIS LEU ALA ASN SER LYS LYS TYR GLN THR PRO SEQRES 10 A 346 PRO HIS GLN ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP SEQRES 11 A 346 LYS ASN ARG ILE TYR ASN SER PRO ILE TYR GLY ALA ASP SEQRES 12 A 346 ILE SER GLY SER LEU PHE ASP GLU ASN THR LYS GLN TRP SEQRES 13 A 346 ASN LEU GLY HIS LEU GLY THR ILE GLN ASP LEU LEU GLU SEQRES 14 A 346 LYS GLU CYS GLY VAL VAL ILE GLU GLY VAL ASN THR PRO SEQRES 15 A 346 TYR LEU TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP SEQRES 16 A 346 HIS THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU SEQRES 17 A 346 HIS LEU GLY GLU PRO LYS THR TRP TYR VAL VAL PRO PRO SEQRES 18 A 346 GLU HIS GLY GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU SEQRES 19 A 346 PHE PRO GLY SER SER ARG GLY CYS GLY ALA PHE LEU ARG SEQRES 20 A 346 HIS LYS VAL ALA LEU ILE SER PRO THR VAL LEU LYS GLU SEQRES 21 A 346 ASN GLY ILE PRO PHE ASN ARG ILE THR GLN GLU ALA GLY SEQRES 22 A 346 GLU PHE MET VAL THR PHE PRO TYR GLY TYR HIS ALA GLY SEQRES 23 A 346 PHE ASN HIS GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE SEQRES 24 A 346 ALA THR PRO ARG TRP ILE ASP TYR GLY LYS MET ALA SER SEQRES 25 A 346 GLN CYS SER CYS GLY GLU ALA ARG VAL THR PHE SER MET SEQRES 26 A 346 ASP ALA PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP SEQRES 27 A 346 LEU TRP LYS ARG GLY GLN ASP ARG HET ZN A 401 1 HET NI A 402 1 HET 5V0 A 403 17 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HET EDO A 414 4 HET EDO A 415 4 HET EDO A 416 4 HET SO4 A 417 5 HET SO4 A 418 5 HET SO4 A 419 5 HET SO4 A 420 5 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM 5V0 2-[(FURAN-2-YLMETHYLAMINO)METHYL]PYRIDINE-4-CARBOXYLIC HETNAM 2 5V0 ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 5V0 C12 H12 N2 O3 FORMUL 5 EDO 13(C2 H6 O2) FORMUL 18 SO4 4(O4 S 2-) FORMUL 22 HOH *344(H2 O) HELIX 1 AA1 GLU A 26 ASN A 29 5 4 HELIX 2 AA2 ASP A 30 GLN A 41 1 12 HELIX 3 AA3 GLY A 42 ALA A 46 5 5 HELIX 4 AA4 VAL A 98 ASN A 106 1 9 HELIX 5 AA5 ASN A 117 ARG A 129 1 13 HELIX 6 AA6 ILE A 130 ASN A 132 5 3 HELIX 7 AA7 THR A 159 GLY A 169 1 11 HELIX 8 AA8 GLU A 194 LEU A 198 5 5 HELIX 9 AA9 PRO A 216 GLU A 218 5 3 HELIX 10 AB1 HIS A 219 PHE A 231 1 13 HELIX 11 AB2 PHE A 231 CYS A 238 1 8 HELIX 12 AB3 ALA A 240 LYS A 245 5 6 HELIX 13 AB4 SER A 250 ASN A 257 1 8 HELIX 14 AB5 ARG A 299 ALA A 307 1 9 HELIX 15 AB6 SER A 320 GLN A 329 1 10 HELIX 16 AB7 GLN A 329 GLN A 340 1 12 SHEET 1 AA110 MET A 19 PHE A 21 0 SHEET 2 AA110 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21 SHEET 3 AA110 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA110 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272 SHEET 5 AA110 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203 SHEET 6 AA110 TYR A 179 GLY A 183 -1 N TYR A 181 O ALA A 290 SHEET 7 AA110 ILE A 135 SER A 141 -1 N GLY A 137 O PHE A 182 SHEET 8 AA110 LEU A 75 ARG A 82 -1 N LEU A 75 O TYR A 136 SHEET 9 AA110 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76 SHEET 10 AA110 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AA2 2 LEU A 70 ILE A 71 0 SHEET 2 AA2 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AA3 4 THR A 188 HIS A 192 0 SHEET 2 AA3 4 TYR A 279 ASN A 284 -1 O HIS A 280 N HIS A 192 SHEET 3 AA3 4 LYS A 210 VAL A 215 -1 N TYR A 213 O ALA A 281 SHEET 4 AA3 4 ASN A 262 GLN A 266 -1 O GLN A 266 N LYS A 210 LINK NE2 HIS A 192 NI NI A 402 1555 1555 2.45 LINK OE2 GLU A 194 NI NI A 402 1555 1555 2.02 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.27 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.12 LINK NE2 HIS A 280 NI NI A 402 1555 1555 2.23 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.31 LINK NI NI A 402 N1 5V0 A 403 1555 1555 2.28 LINK NI NI A 402 N 5V0 A 403 1555 1555 2.20 LINK NI NI A 402 O HOH A 529 1555 1555 2.20 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 5V0 A 403 SITE 2 AC2 5 HOH A 529 SITE 1 AC3 17 TYR A 136 TYR A 181 PHE A 189 HIS A 192 SITE 2 AC3 17 GLU A 194 SER A 200 ASN A 202 LYS A 210 SITE 3 AC3 17 TRP A 212 HIS A 280 ALA A 292 ILE A 293 SITE 4 AC3 17 ASN A 294 NI A 402 HOH A 510 HOH A 529 SITE 5 AC3 17 HOH A 766 SITE 1 AC4 7 GLU A 224 ARG A 228 GLY A 239 ALA A 240 SITE 2 AC4 7 PHE A 241 LEU A 242 HOH A 742 SITE 1 AC5 5 GLU A 27 TYR A 37 HOH A 544 HOH A 591 SITE 2 AC5 5 HOH A 592 SITE 1 AC6 8 PHE A 31 LYS A 150 GLN A 151 TRP A 152 SITE 2 AC6 8 ASN A 153 HOH A 501 HOH A 523 HOH A 564 SITE 1 AC7 6 LYS A 50 ILE A 264 THR A 265 GLU A 267 SITE 2 AC7 6 EDO A 415 HOH A 752 SITE 1 AC8 7 ALA A 83 GLY A 84 TRP A 126 SER A 250 SITE 2 AC8 7 THR A 252 HOH A 514 HOH A 565 SITE 1 AC9 4 HIS A 103 ASN A 106 HOH A 511 HOH A 553 SITE 1 AD1 3 PRO A 251 LYS A 255 ARG A 263 SITE 1 AD2 5 ILE A 20 PHE A 21 HOH A 547 HOH A 585 SITE 2 AD2 5 HOH A 782 SITE 1 AD3 1 PHE A 261 SITE 1 AD4 4 HIS A 22 GLU A 27 TYR A 34 HOH A 520 SITE 1 AD5 6 SER A 80 GLY A 81 VAL A 85 THR A 87 SITE 2 AD5 6 CYS A 168 HOH A 503 SITE 1 AD6 5 PHE A 118 GLU A 122 ILE A 264 THR A 265 SITE 2 AD6 5 EDO A 407 SITE 1 AD7 8 ASN A 13 GLY A 258 ILE A 259 PRO A 260 SITE 2 AD7 8 HOH A 547 HOH A 597 HOH A 632 HOH A 651 SITE 1 AD8 6 ARG A 60 GLU A 61 THR A 62 ASN A 65 SITE 2 AD8 6 HOH A 534 HOH A 537 SITE 1 AD9 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 1 AE1 7 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 AE1 7 LYS A 186 HOH A 513 HOH A 736 SITE 1 AE2 2 TYR A 303 MET A 306 CRYST1 71.280 71.280 150.360 90.00 90.00 90.00 P 43 21 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 0.014029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006651 0.00000