HEADER OXIDOREDUCTASE 10-JUN-07 2Q8C TITLE CRYSTAL STRUCTURE OF JMJD2A IN TERNARY COMPLEX WITH AN HISTONE H3K9ME3 TITLE 2 PEPTIDE AND 2-OXOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: JUMONJI DOMAIN; COMPND 5 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE 3 PEPTIDE; COMPND 10 CHAIN: F, G; COMPND 11 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: JMJD2A, JHDM3A, JMJD2, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21DE3PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS HISTONE DEMETHYLASE, HYDROXYLASE, JUMONJI, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-F.COUTURE,E.COLLAZO,P.ORTIZ-TELLO,J.S.BRUNZELLE,R.C.TRIEVEL REVDAT 6 30-AUG-23 2Q8C 1 REMARK SEQADV LINK REVDAT 5 24-JAN-18 2Q8C 1 AUTHOR REVDAT 4 13-JUL-11 2Q8C 1 VERSN REVDAT 3 24-FEB-09 2Q8C 1 VERSN REVDAT 2 29-JAN-08 2Q8C 1 JRNL REVDAT 1 03-JUL-07 2Q8C 0 JRNL AUTH J.F.COUTURE,E.COLLAZO,P.A.ORTIZ-TELLO,J.S.BRUNZELLE, JRNL AUTH 2 R.C.TRIEVEL JRNL TITL SPECIFICITY AND MECHANISM OF JMJD2A, A JRNL TITL 2 TRIMETHYLLYSINE-SPECIFIC HISTONE DEMETHYLASE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 689 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17589523 JRNL DOI 10.1038/NSMB1273 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 54535 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2762 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3439 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5607 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 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): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.563 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5816 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7879 ; 1.253 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 688 ; 5.920 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 281 ;32.558 ;22.989 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 943 ;16.076 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.616 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 806 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4517 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2622 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3952 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 279 ; 0.157 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.016 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.124 ; 0.200 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): 3560 ; 0.691 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5563 ; 1.128 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2655 ; 1.662 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2316 ; 2.467 ; 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 : 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 REMARK 4 REMARK 4 2Q8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54585 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 28.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.03000 REMARK 200 FOR THE DATA SET : 39.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50600 REMARK 200 R SYM FOR SHELL (I) : 0.47600 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2GP5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.44350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.56050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.44350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.56050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THIS PROTEIN IS ACTIVE AS A MONOMER WITH TWO MOLECULES IN REMARK 300 THE ASYMMETRIC UNIT. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 348 REMARK 465 GLU A 349 REMARK 465 ALA A 350 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 GLU B 6 REMARK 465 THR B 7 REMARK 465 LEU B 8 REMARK 465 ASN B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 THR B 347 REMARK 465 PRO B 348 REMARK 465 GLU B 349 REMARK 465 ALA B 350 REMARK 465 ALA F 1 REMARK 465 ARG F 2 REMARK 465 THR F 3 REMARK 465 LYS F 4 REMARK 465 GLN F 5 REMARK 465 THR F 6 REMARK 465 THR F 11 REMARK 465 GLY F 12 REMARK 465 GLY F 13 REMARK 465 LYS F 14 REMARK 465 ALA F 15 REMARK 465 ALA G 1 REMARK 465 ARG G 2 REMARK 465 THR G 3 REMARK 465 LYS G 4 REMARK 465 GLN G 5 REMARK 465 LYS G 14 REMARK 465 ALA G 15 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 51 CG CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 90 CD CE NZ REMARK 470 ARG A 95 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 104 CG OD1 OD2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 GLN A 232 CB CG CD OE1 NE2 REMARK 470 GLU A 235 CG CD OE1 OE2 REMARK 470 LYS A 310 CB CG CD CE NZ REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 LYS B 51 CD CE NZ REMARK 470 LYS B 54 CD CE NZ REMARK 470 LYS B 89 CD CE NZ REMARK 470 ASP B 104 CG OD1 OD2 REMARK 470 ARG B 110 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 162 CB CG CD CE NZ REMARK 470 LYS B 310 CB CG CD CE NZ REMARK 470 LYS B 333 CG CD CE NZ REMARK 470 LYS B 336 CG CD CE NZ REMARK 470 THR G 11 CB OG1 CG2 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 B 169 NH1 ARG G 8 2.16 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 SER A 112 -77.33 -87.03 REMARK 500 ARG A 152 74.32 -161.52 REMARK 500 MET A 192 18.48 58.02 REMARK 500 ASN B 128 70.48 47.32 REMARK 500 ARG B 152 69.40 -164.82 REMARK 500 LYS B 182 3.25 81.34 REMARK 500 MET B 192 19.48 56.93 REMARK 500 PHE B 227 73.16 -119.24 REMARK 500 ASP B 311 22.98 -78.02 REMARK 500 ALA G 7 96.99 52.54 REMARK 500 THR G 11 80.06 -155.24 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 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE1 99.2 REMARK 620 3 HIS A 276 NE2 91.3 88.9 REMARK 620 4 AKG A 503 O5 79.0 150.8 120.2 REMARK 620 5 AKG A 503 O2 161.5 97.8 96.1 82.7 REMARK 620 6 HOH A 609 O 83.3 83.2 169.5 67.6 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 112.3 REMARK 620 3 CYS A 306 SG 111.4 113.2 REMARK 620 4 CYS A 308 SG 112.6 94.5 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 502 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE1 98.8 REMARK 620 3 HIS B 276 NE2 91.3 87.2 REMARK 620 4 AKG B 504 O2 164.7 96.5 90.2 REMARK 620 5 AKG B 504 O5 84.7 168.2 104.1 80.2 REMARK 620 6 HOH B 600 O 79.8 87.4 168.8 100.2 82.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 116.5 REMARK 620 3 CYS B 306 SG 109.1 110.1 REMARK 620 4 CYS B 308 SG 115.8 89.8 114.4 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q8D RELATED DB: PDB REMARK 900 SAME PROTEIN WITH SIN REMARK 900 RELATED ID: 2Q8E RELATED DB: PDB REMARK 900 SAME PROTEIN WITH OGA DBREF 2Q8C A 1 350 UNP O75164 JHD3A_HUMAN 1 350 DBREF 2Q8C B 1 350 UNP O75164 JHD3A_HUMAN 1 350 DBREF 2Q8C F 1 15 PDB 2Q8C 2Q8C 1 15 DBREF 2Q8C G 1 15 PDB 2Q8C 2Q8C 1 15 SEQADV 2Q8C GLY A -1 UNP O75164 CLONING ARTIFACT SEQADV 2Q8C SER A 0 UNP O75164 CLONING ARTIFACT SEQADV 2Q8C GLY B -1 UNP O75164 CLONING ARTIFACT SEQADV 2Q8C SER B 0 UNP O75164 CLONING ARTIFACT SEQRES 1 A 352 GLY SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER SEQRES 2 A 352 ALA ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE SEQRES 3 A 352 ARG ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN SEQRES 4 A 352 GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO SEQRES 5 A 352 LYS GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP SEQRES 6 A 352 ASP LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR SEQRES 7 A 352 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 A 352 LYS ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SEQRES 9 A 352 SER ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU SEQRES 10 A 352 GLU LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN SEQRES 11 A 352 PRO PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR SEQRES 12 A 352 GLU LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG SEQRES 13 A 352 THR ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR SEQRES 14 A 352 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 A 352 TRP LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 A 352 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 A 352 SER TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 A 352 GLU ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SEQRES 19 A 352 SER CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 A 352 SER PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP SEQRES 21 A 352 LYS VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 A 352 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 A 352 CYS ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE SEQRES 24 A 352 GLU TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS SEQRES 25 A 352 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS SEQRES 26 A 352 PHE GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS SEQRES 27 A 352 ASP ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU SEQRES 28 A 352 ALA SEQRES 1 B 352 GLY SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER SEQRES 2 B 352 ALA ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE SEQRES 3 B 352 ARG ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN SEQRES 4 B 352 GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO SEQRES 5 B 352 LYS GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP SEQRES 6 B 352 ASP LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR SEQRES 7 B 352 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 B 352 LYS ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SEQRES 9 B 352 SER ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU SEQRES 10 B 352 GLU LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN SEQRES 11 B 352 PRO PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR SEQRES 12 B 352 GLU LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG SEQRES 13 B 352 THR ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR SEQRES 14 B 352 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 B 352 TRP LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 B 352 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 B 352 SER TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 B 352 GLU ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SEQRES 19 B 352 SER CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 B 352 SER PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP SEQRES 21 B 352 LYS VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 B 352 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 B 352 CYS ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE SEQRES 24 B 352 GLU TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS SEQRES 25 B 352 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS SEQRES 26 B 352 PHE GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS SEQRES 27 B 352 ASP ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU SEQRES 28 B 352 ALA SEQRES 1 F 15 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 F 15 LYS ALA SEQRES 1 G 15 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 G 15 LYS ALA MODRES 2Q8C M3L F 9 LYS N-TRIMETHYLLYSINE MODRES 2Q8C M3L G 9 LYS N-TRIMETHYLLYSINE HET M3L F 9 12 HET M3L G 9 12 HET NI A 501 1 HET ZN A 505 1 HET AKG A 503 10 HET NI B 502 1 HET ZN B 506 1 HET AKG B 504 10 HETNAM M3L N-TRIMETHYLLYSINE HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 3 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 NI 2(NI 2+) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 AKG 2(C5 H6 O5) FORMUL 11 HOH *199(H2 O) HELIX 1 1 SER A 3 LEU A 8 1 6 HELIX 2 2 THR A 20 ARG A 25 1 6 HELIX 3 3 ASN A 26 GLN A 37 1 12 HELIX 4 4 GLY A 38 ALA A 42 5 5 HELIX 5 5 VAL A 94 SER A 103 1 10 HELIX 6 6 GLU A 113 LEU A 125 1 13 HELIX 7 7 THR A 155 LEU A 157 5 3 HELIX 8 8 ASP A 158 GLY A 165 1 8 HELIX 9 9 GLU A 190 LEU A 194 5 5 HELIX 10 10 PRO A 212 GLU A 214 5 3 HELIX 11 11 HIS A 215 PHE A 227 1 13 HELIX 12 12 PHE A 227 CYS A 234 1 8 HELIX 13 13 ALA A 236 LYS A 241 5 6 HELIX 14 14 SER A 246 TYR A 253 1 8 HELIX 15 15 ARG A 295 ALA A 303 1 9 HELIX 16 16 MET A 317 GLN A 325 1 9 HELIX 17 17 ARG A 328 ALA A 334 1 7 HELIX 18 18 THR B 20 ARG B 25 1 6 HELIX 19 19 ASN B 26 GLN B 37 1 12 HELIX 20 20 GLY B 38 ALA B 42 5 5 HELIX 21 21 VAL B 94 ASN B 102 1 9 HELIX 22 22 GLU B 113 LEU B 125 1 13 HELIX 23 23 LEU B 157 GLY B 165 1 9 HELIX 24 24 GLU B 190 LEU B 194 5 5 HELIX 25 25 PRO B 212 GLU B 214 5 3 HELIX 26 26 HIS B 215 PHE B 227 1 13 HELIX 27 27 PHE B 227 CYS B 234 1 8 HELIX 28 28 ALA B 236 LYS B 241 5 6 HELIX 29 29 SER B 246 TYR B 253 1 8 HELIX 30 30 ARG B 295 ALA B 303 1 9 HELIX 31 31 MET B 317 GLN B 325 1 9 HELIX 32 32 ARG B 328 ALA B 334 1 7 SHEET 1 A10 MET A 15 PHE A 17 0 SHEET 2 A10 LEU A 44 VAL A 47 1 O LYS A 46 N PHE A 17 SHEET 3 A10 PHE A 267 THR A 270 -1 O ILE A 269 N ALA A 45 SHEET 4 A10 TYR A 195 GLY A 203 -1 N ASN A 198 O MET A 268 SHEET 5 A10 ASN A 284 PHE A 291 -1 O GLU A 287 N TYR A 199 SHEET 6 A10 TYR A 175 GLY A 179 -1 N TYR A 177 O ALA A 286 SHEET 7 A10 ILE A 131 ASN A 137 -1 N VAL A 136 O LEU A 176 SHEET 8 A10 ILE A 71 GLN A 78 -1 N ILE A 71 O TYR A 132 SHEET 9 A10 LEU A 81 GLN A 88 -1 O TYR A 85 N LEU A 74 SHEET 10 A10 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 B 2 VAL A 66 ILE A 67 0 SHEET 2 B 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 C 4 SER A 184 HIS A 188 0 SHEET 2 C 4 TYR A 275 ASN A 280 -1 O GLY A 278 N PHE A 185 SHEET 3 C 4 LYS A 206 VAL A 211 -1 N TYR A 209 O ALA A 277 SHEET 4 C 4 ASP A 258 GLN A 262 -1 O VAL A 260 N TRP A 208 SHEET 1 D10 MET B 15 PHE B 17 0 SHEET 2 D10 LEU B 44 VAL B 47 1 O LYS B 46 N MET B 15 SHEET 3 D10 PHE B 267 THR B 270 -1 O ILE B 269 N ALA B 45 SHEET 4 D10 TYR B 195 GLY B 203 -1 N ASN B 198 O MET B 268 SHEET 5 D10 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 D10 TYR B 175 GLY B 179 -1 N TYR B 175 O SER B 288 SHEET 7 D10 ILE B 131 ASN B 137 -1 N VAL B 136 O LEU B 176 SHEET 8 D10 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 D10 LEU B 81 GLN B 88 -1 O TYR B 85 N LEU B 74 SHEET 10 D10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 E 2 VAL B 66 ILE B 67 0 SHEET 2 E 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 F 4 SER B 184 HIS B 188 0 SHEET 2 F 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 F 4 LYS B 206 VAL B 211 -1 N SER B 207 O PHE B 279 SHEET 4 F 4 ASP B 258 GLN B 262 -1 O GLN B 262 N LYS B 206 LINK C ARG F 8 N M3L F 9 1555 1555 1.33 LINK C M3L F 9 N SER F 10 1555 1555 1.33 LINK C ARG G 8 N M3L G 9 1555 1555 1.33 LINK C M3L G 9 N SER G 10 1555 1555 1.33 LINK NE2 HIS A 188 NI NI A 501 1555 1555 2.15 LINK OE1 GLU A 190 NI NI A 501 1555 1555 2.15 LINK SG CYS A 234 ZN ZN A 505 1555 1555 2.22 LINK NE2 HIS A 240 ZN ZN A 505 1555 1555 2.07 LINK NE2 HIS A 276 NI NI A 501 1555 1555 2.01 LINK SG CYS A 306 ZN ZN A 505 1555 1555 1.79 LINK SG CYS A 308 ZN ZN A 505 1555 1555 2.46 LINK NI NI A 501 O5 AKG A 503 1555 1555 2.49 LINK NI NI A 501 O2 AKG A 503 1555 1555 1.52 LINK NI NI A 501 O HOH A 609 1555 1555 1.89 LINK NE2 HIS B 188 NI NI B 502 1555 1555 2.13 LINK OE1 GLU B 190 NI NI B 502 1555 1555 2.17 LINK SG CYS B 234 ZN ZN B 506 1555 1555 2.24 LINK NE2 HIS B 240 ZN ZN B 506 1555 1555 2.04 LINK NE2 HIS B 276 NI NI B 502 1555 1555 2.07 LINK SG CYS B 306 ZN ZN B 506 1555 1555 1.81 LINK SG CYS B 308 ZN ZN B 506 1555 1555 2.34 LINK NI NI B 502 O2 AKG B 504 1555 1555 1.76 LINK NI NI B 502 O5 AKG B 504 1555 1555 2.38 LINK NI NI B 502 O HOH B 600 1555 1555 2.08 CISPEP 1 THR G 11 GLY G 12 0 2.74 SITE 1 AC1 5 HIS A 188 GLU A 190 HIS A 276 AKG A 503 SITE 2 AC1 5 HOH A 609 SITE 1 AC2 5 HIS B 188 GLU B 190 HIS B 276 AKG B 504 SITE 2 AC2 5 HOH B 600 SITE 1 AC3 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC4 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC5 12 TYR A 132 TYR A 177 HIS A 188 GLU A 190 SITE 2 AC5 12 SER A 196 ASN A 198 LYS A 206 TRP A 208 SITE 3 AC5 12 HIS A 276 NI A 501 HOH A 540 HOH A 609 SITE 1 AC6 12 TYR B 132 PHE B 185 HIS B 188 GLU B 190 SITE 2 AC6 12 SER B 196 ASN B 198 LYS B 206 TRP B 208 SITE 3 AC6 12 HIS B 276 NI B 502 HOH B 595 HOH B 600 CRYST1 100.887 149.121 57.056 90.00 90.00 90.00 P 21 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 0.009912 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017527 0.00000