HEADER OXIDOREDUCTASE 22-OCT-12 4HOO TITLE CRYSTAL STRUCTURE OF HUMAN JMJD2D/KDM4D APOENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 12-341; 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; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: JHDM3D, JMJD2D, KDM4D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(ROSETTA 2); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLAMSID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHT4 KEYWDS JUMONJI C DEMETHYLASE, JMJD2/KDM4 FAMILY, BETA BARREL FOLD, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KRISHNAN,R.C.TRIEVEL REVDAT 5 20-SEP-23 4HOO 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 4HOO 1 REMARK REVDAT 3 30-JAN-13 4HOO 1 JRNL REVDAT 2 02-JAN-13 4HOO 1 JRNL REVDAT 1 21-NOV-12 4HOO 0 JRNL AUTH S.KRISHNAN,R.C.TRIEVEL JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF JMJD2D REVEALS JRNL TITL 2 MOLECULAR BASIS FOR SITE-SPECIFIC DEMETHYLATION AMONG JMJD2 JRNL TITL 3 DEMETHYLASES. JRNL REF STRUCTURE V. 21 98 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23219879 JRNL DOI 10.1016/J.STR.2012.10.018 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 25819 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1311 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1649 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5173 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.74000 REMARK 3 B22 (A**2) : 5.74000 REMARK 3 B33 (A**2) : -8.61000 REMARK 3 B12 (A**2) : 2.87000 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): 0.709 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.301 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.250 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5353 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7287 ; 1.495 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 660 ; 7.144 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 255 ;35.434 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 796 ;16.543 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.683 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 754 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4219 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3284 ; 0.549 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5244 ; 0.988 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2069 ; 1.235 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2040 ; 1.969 ; 4.500 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 : 2 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 12 A 341 REMARK 3 ORIGIN FOR THE GROUP (A): -9.8280 7.1350 0.6010 REMARK 3 T TENSOR REMARK 3 T11: 0.0203 T22: 0.0140 REMARK 3 T33: 0.7665 T12: -0.0053 REMARK 3 T13: -0.0222 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 3.0233 L22: 1.9639 REMARK 3 L33: 1.4785 L12: 0.0704 REMARK 3 L13: -0.6822 L23: -0.1826 REMARK 3 S TENSOR REMARK 3 S11: -0.0893 S12: 0.1760 S13: -0.0431 REMARK 3 S21: -0.1421 S22: 0.0616 S23: -0.0127 REMARK 3 S31: -0.0637 S32: -0.0959 S33: 0.0278 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 12 B 341 REMARK 3 ORIGIN FOR THE GROUP (A): -25.3470 16.3350 49.1060 REMARK 3 T TENSOR REMARK 3 T11: 0.0113 T22: 0.0180 REMARK 3 T33: 0.7483 T12: -0.0047 REMARK 3 T13: -0.0146 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 2.4934 L22: 2.4748 REMARK 3 L33: 1.1388 L12: -0.6635 REMARK 3 L13: -0.3846 L23: 0.2554 REMARK 3 S TENSOR REMARK 3 S11: -0.0208 S12: -0.1655 S13: -0.0458 REMARK 3 S21: 0.1541 S22: -0.0064 S23: 0.0353 REMARK 3 S31: -0.0222 S32: 0.1003 S33: 0.0271 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 : RESIDUAL ONLY REMARK 4 REMARK 4 4HOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25850 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.495 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 4HON REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CALCIUM ACETATE, 0.1M HEPES PH REMARK 280 7.5, 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 90.68533 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 45.34267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 350 REMARK 350 BIOMOLECULE: 2 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: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 235 REMARK 465 ARG A 236 REMARK 465 GLY A 237 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 GLN A 12 CG CD OE1 NE2 REMARK 470 GLU A 26 CG CD OE1 OE2 REMARK 470 ARG A 45 NE CZ NH1 NH2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ASP A 64 CG OD1 OD2 REMARK 470 ASN A 65 CG OD1 ND2 REMARK 470 ILE A 66 CG1 CG2 CD1 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 LYS A 91 CE NZ REMARK 470 LYS A 92 NZ REMARK 470 ARG A 102 NE CZ NH1 NH2 REMARK 470 LYS A 108 CD CE NZ REMARK 470 GLN A 111 CG CD OE1 NE2 REMARK 470 LYS A 127 CD CE NZ REMARK 470 LYS A 166 CG CD CE NZ REMARK 470 CYS A 238 SG REMARK 470 LYS A 255 CD CE NZ REMARK 470 ASP A 341 CG OD1 OD2 REMARK 470 LYS B 25 CD CE NZ REMARK 470 GLU B 26 CG CD OE1 OE2 REMARK 470 ARG B 45 NE CZ NH1 NH2 REMARK 470 LYS B 55 CE NZ REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 LYS B 58 CG CD CE NZ REMARK 470 GLU B 61 CG CD OE1 OE2 REMARK 470 ASN B 65 CG OD1 ND2 REMARK 470 ILE B 66 CG1 CG2 CD1 REMARK 470 TYR B 89 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 92 NZ REMARK 470 LYS B 108 CD CE NZ REMARK 470 GLN B 111 CG CD OE1 NE2 REMARK 470 GLU B 119 CG CD OE1 OE2 REMARK 470 ASP B 146 CG OD1 OD2 REMARK 470 GLU B 147 CG CD OE1 OE2 REMARK 470 ASN B 148 CG OD1 ND2 REMARK 470 LYS B 166 CG CD CE NZ REMARK 470 ARG B 225 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 236 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 255 CD CE NZ REMARK 470 MET B 306 CG SD CE REMARK 470 GLU B 314 CG CD OE1 OE2 REMARK 470 ARG B 316 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 317 CG1 CG2 REMARK 470 GLU B 331 CG CD OE1 OE2 REMARK 470 ASP B 341 CG OD1 OD2 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 O CYS B 289 O HOH B 580 2.11 REMARK 500 O ASP B 341 O HOH B 524 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 CD2 HIS A 22 CG2 THR B 318 2554 1.75 REMARK 500 NE2 HIS A 22 CG2 THR B 318 2554 2.11 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 ASN A 13 70.37 47.49 REMARK 500 ASN A 65 16.43 56.48 REMARK 500 GLU A 68 47.52 -85.98 REMARK 500 ARG A 82 -173.63 177.86 REMARK 500 VAL A 175 -62.29 -96.75 REMARK 500 LYS A 186 -18.16 88.15 REMARK 500 GLN A 340 -106.85 -130.27 REMARK 500 HIS B 22 76.04 -118.63 REMARK 500 ARG B 82 169.89 174.69 REMARK 500 ASP B 162 -8.48 -58.75 REMARK 500 LYS B 186 -17.79 80.75 REMARK 500 PRO B 276 129.29 -39.52 REMARK 500 THR B 318 132.85 -175.17 REMARK 500 GLN B 340 -75.97 -80.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR B 318 PHE B 319 134.82 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 NI A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 80.3 REMARK 620 3 HIS A 280 NE2 86.9 73.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 244 NE2 REMARK 620 2 CYS A 310 SG 124.0 REMARK 620 3 CYS A 312 SG 99.9 103.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 192 NE2 REMARK 620 2 GLU B 194 OE2 82.1 REMARK 620 3 HIS B 280 NE2 84.6 71.2 REMARK 620 4 HOH B 502 O 163.5 113.9 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 238 SG REMARK 620 2 HIS B 244 NE2 126.0 REMARK 620 3 CYS B 310 SG 78.8 122.9 REMARK 620 4 CYS B 312 SG 125.9 100.9 98.6 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 NI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 402 DBREF 4HOO A 12 341 UNP Q6B0I6 KDM4D_HUMAN 12 341 DBREF 4HOO B 12 341 UNP Q6B0I6 KDM4D_HUMAN 12 341 SEQADV 4HOO ALA A 93 UNP Q6B0I6 LYS 93 ENGINEERED MUTATION SEQADV 4HOO ALA A 94 UNP Q6B0I6 LYS 94 ENGINEERED MUTATION SEQADV 4HOO ALA B 93 UNP Q6B0I6 LYS 93 ENGINEERED MUTATION SEQADV 4HOO ALA B 94 UNP Q6B0I6 LYS 94 ENGINEERED MUTATION SEQRES 1 A 330 GLN ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR SEQRES 2 A 330 LYS GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR SEQRES 3 A 330 MET GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS SEQRES 4 A 330 ILE ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR SEQRES 5 A 330 ASP ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN SEQRES 6 A 330 GLN VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR SEQRES 7 A 330 HIS LYS LYS ALA ALA ALA MET THR VAL GLY GLU TYR ARG SEQRES 8 A 330 HIS LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS SEQRES 9 A 330 GLN ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN SEQRES 10 A 330 ARG ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER SEQRES 11 A 330 GLY SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU SEQRES 12 A 330 GLY HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU SEQRES 13 A 330 CYS GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU SEQRES 14 A 330 TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS THR SEQRES 15 A 330 GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU SEQRES 16 A 330 GLY GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS SEQRES 17 A 330 GLY GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO SEQRES 18 A 330 GLY SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS SEQRES 19 A 330 VAL ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY SEQRES 20 A 330 ILE PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE SEQRES 21 A 330 MET VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN SEQRES 22 A 330 HIS GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR SEQRES 23 A 330 PRO ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SEQRES 24 A 330 SER CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA SEQRES 25 A 330 PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP SEQRES 26 A 330 LYS ARG GLY GLN ASP SEQRES 1 B 330 GLN ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR SEQRES 2 B 330 LYS GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR SEQRES 3 B 330 MET GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS SEQRES 4 B 330 ILE ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR SEQRES 5 B 330 ASP ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN SEQRES 6 B 330 GLN VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR SEQRES 7 B 330 HIS LYS LYS ALA ALA ALA MET THR VAL GLY GLU TYR ARG SEQRES 8 B 330 HIS LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS SEQRES 9 B 330 GLN ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN SEQRES 10 B 330 ARG ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER SEQRES 11 B 330 GLY SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU SEQRES 12 B 330 GLY HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU SEQRES 13 B 330 CYS GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU SEQRES 14 B 330 TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS THR SEQRES 15 B 330 GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU SEQRES 16 B 330 GLY GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS SEQRES 17 B 330 GLY GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO SEQRES 18 B 330 GLY SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS SEQRES 19 B 330 VAL ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY SEQRES 20 B 330 ILE PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE SEQRES 21 B 330 MET VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN SEQRES 22 B 330 HIS GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR SEQRES 23 B 330 PRO ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SEQRES 24 B 330 SER CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA SEQRES 25 B 330 PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP SEQRES 26 B 330 LYS ARG GLY GLN ASP HET NI A 401 1 HET ZN A 402 1 HET ACT A 403 4 HET ACT A 404 4 HET NI B 401 1 HET ZN B 402 1 HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM ACT ACETATE ION FORMUL 3 NI 2(NI 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 9 HOH *153(H2 O) HELIX 1 1 ASP A 30 GLN A 41 1 12 HELIX 2 2 GLY A 42 ALA A 46 5 5 HELIX 3 3 VAL A 98 ALA A 105 1 8 HELIX 4 4 ASN A 117 ASN A 128 1 12 HELIX 5 5 THR A 159 GLN A 161 5 3 HELIX 6 6 ASP A 162 GLY A 169 1 8 HELIX 7 7 GLU A 194 LEU A 198 5 5 HELIX 8 8 PRO A 216 GLU A 218 5 3 HELIX 9 9 HIS A 219 PHE A 231 1 13 HELIX 10 10 ALA A 240 LYS A 245 5 6 HELIX 11 11 SER A 250 ASN A 257 1 8 HELIX 12 12 THR A 297 ARG A 299 5 3 HELIX 13 13 TRP A 300 LYS A 305 1 6 HELIX 14 14 MET A 321 GLN A 329 1 9 HELIX 15 15 ARG A 332 GLY A 339 1 8 HELIX 16 16 LYS B 25 ASN B 29 5 5 HELIX 17 17 ASP B 30 GLN B 41 1 12 HELIX 18 18 GLY B 42 ALA B 46 5 5 HELIX 19 19 TYR B 63 GLU B 68 5 6 HELIX 20 20 VAL B 98 ASN B 106 1 9 HELIX 21 21 ASN B 117 ARG B 129 1 13 HELIX 22 22 THR B 159 GLN B 161 5 3 HELIX 23 23 ASP B 162 GLY B 169 1 8 HELIX 24 24 GLU B 194 LEU B 198 5 5 HELIX 25 25 PRO B 216 GLU B 218 5 3 HELIX 26 26 HIS B 219 PHE B 231 1 13 HELIX 27 27 ALA B 240 LYS B 245 5 6 HELIX 28 28 SER B 250 ASN B 257 1 8 HELIX 29 29 THR B 297 ARG B 299 5 3 HELIX 30 30 TRP B 300 ALA B 307 1 8 HELIX 31 31 MET B 321 GLN B 329 1 9 HELIX 32 32 ARG B 332 ASP B 341 1 10 SHEET 1 A10 MET A 19 PHE A 21 0 SHEET 2 A10 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21 SHEET 3 A10 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 A10 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272 SHEET 5 A10 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203 SHEET 6 A10 TYR A 179 GLY A 183 -1 N TYR A 181 O ALA A 290 SHEET 7 A10 ILE A 135 SER A 141 -1 N ILE A 140 O LEU A 180 SHEET 8 A10 LEU A 75 ARG A 82 -1 N LEU A 75 O TYR A 136 SHEET 9 A10 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76 SHEET 10 A10 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 B 2 LEU A 70 ILE A 71 0 SHEET 2 B 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 C 4 THR A 188 HIS A 192 0 SHEET 2 C 4 HIS A 280 ASN A 284 -1 O GLY A 282 N PHE A 189 SHEET 3 C 4 LYS A 210 VAL A 214 -1 N TYR A 213 O ALA A 281 SHEET 4 C 4 ASN A 262 GLN A 266 -1 O GLN A 266 N LYS A 210 SHEET 1 D10 MET B 19 PHE B 21 0 SHEET 2 D10 LEU B 48 ILE B 51 1 O LYS B 50 N MET B 19 SHEET 3 D10 PHE B 271 THR B 274 -1 O PHE B 271 N ILE B 51 SHEET 4 D10 TYR B 199 GLY B 207 -1 N ASN B 202 O MET B 272 SHEET 5 D10 ASN B 288 PHE B 295 -1 O GLU B 291 N TYR B 203 SHEET 6 D10 TYR B 179 GLY B 183 -1 N TYR B 181 O ALA B 290 SHEET 7 D10 ILE B 135 SER B 141 -1 N GLY B 137 O PHE B 182 SHEET 8 D10 LEU B 75 ARG B 82 -1 N LEU B 75 O TYR B 136 SHEET 9 D10 VAL B 85 LYS B 92 -1 O LYS B 91 N GLN B 76 SHEET 10 D10 ALA B 247 ILE B 249 -1 O LEU B 248 N PHE B 86 SHEET 1 E 2 LEU B 70 ILE B 71 0 SHEET 2 E 2 MET B 96 THR B 97 -1 O MET B 96 N ILE B 71 SHEET 1 F 4 THR B 188 HIS B 192 0 SHEET 2 F 4 HIS B 280 ASN B 284 -1 O GLY B 282 N PHE B 189 SHEET 3 F 4 LYS B 210 VAL B 214 -1 N TYR B 213 O ALA B 281 SHEET 4 F 4 ASN B 262 GLN B 266 -1 O GLN B 266 N LYS B 210 SSBOND 1 CYS B 238 CYS B 310 1555 1555 2.92 LINK NE2 HIS A 192 NI NI A 401 1555 1555 2.20 LINK OE2 GLU A 194 NI NI A 401 1555 1555 1.80 LINK NE2 HIS A 244 ZN ZN A 402 1555 1555 2.54 LINK NE2 HIS A 280 NI NI A 401 1555 1555 2.24 LINK SG CYS A 310 ZN ZN A 402 1555 1555 2.37 LINK SG CYS A 312 ZN ZN A 402 1555 1555 2.56 LINK NE2 HIS B 192 NI NI B 401 1555 1555 2.34 LINK OE2 GLU B 194 NI NI B 401 1555 1555 1.85 LINK SG CYS B 238 ZN ZN B 402 1555 1555 2.46 LINK NE2 HIS B 244 ZN ZN B 402 1555 1555 2.45 LINK NE2 HIS B 280 NI NI B 401 1555 1555 2.24 LINK SG CYS B 310 ZN ZN B 402 1555 1555 2.13 LINK SG CYS B 312 ZN ZN B 402 1555 1555 2.35 LINK NI NI B 401 O HOH B 502 1555 1555 2.76 SITE 1 AC1 5 HIS A 192 GLU A 194 HIS A 280 HOH A 507 SITE 2 AC1 5 HOH A 526 SITE 1 AC2 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC3 4 ASN A 15 ASN A 17 PHE A 261 ASN A 262 SITE 1 AC4 2 GLU A 27 HOH A 528 SITE 1 AC5 4 HIS B 192 GLU B 194 HIS B 280 HOH B 502 SITE 1 AC6 4 CYS B 238 HIS B 244 CYS B 310 CYS B 312 CRYST1 73.119 73.119 136.028 90.00 90.00 120.00 P 32 6 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 0.013676 0.007896 0.000000 0.00000 SCALE2 0.000000 0.015792 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007351 0.00000