HEADER OXIDOREDUCTASE/DNA 21-MAY-11 3S5A TITLE ABH2 CROSS-LINKED TO UNDAMAGED DSDNA-2 WITH COFACTORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DIOXYGENASE DOMAIN (UNP RESIDUES 56-258); COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 2, OXY DC1; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*TP*GP*TP*CP*TP*CP*AP*CP*TP*GP*TP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*TP*CP*GP*AP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3'; COMPND 15 CHAIN: C; COMPND 16 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: ABH2, ALKBH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, DOUBLE HELIX, JELLY-ROLL FOLD, DIOXYGENASE, DNA KEYWDS 2 BINDING, CROSS-LINKING, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,B.CHEN,B.QI,B.RAMIREZ,W.ZHANG,G.JIA,L.ZHANG,C.Q.LI,A.R.DINNER, AUTHOR 2 C.-G.YANG,C.HE REVDAT 3 20-MAR-24 3S5A 1 REMARK SEQADV LINK REVDAT 2 03-JUL-13 3S5A 1 JRNL REVDAT 1 06-JUN-12 3S5A 0 JRNL AUTH C.YI,B.CHEN,B.QI,W.ZHANG,G.JIA,L.ZHANG,C.J.LI,A.R.DINNER, JRNL AUTH 2 C.G.YANG,C.HE JRNL TITL DUPLEX INTERROGATION BY A DIRECT DNA REPAIR PROTEIN IN JRNL TITL 2 SEARCH OF BASE DAMAGE JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 671 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22659876 JRNL DOI 10.1038/NSMB.2320 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 37531 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2726 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1636 REMARK 3 NUCLEIC ACID ATOMS : 566 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 338 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -1.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.149 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.591 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2419 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3397 ; 1.487 ; 2.254 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 219 ; 6.619 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;31.473 ;21.807 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;13.455 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.120 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1686 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1001 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1569 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 296 ; 0.158 ; 0.200 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): 20 ; 0.122 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.153 ; 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): 1088 ; 1.205 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1732 ; 1.870 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1693 ; 2.421 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1665 ; 3.366 ; 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): 2781 ; 2.038 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 339 ; 5.097 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2301 ; 4.454 ; 3.000 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 REMARK 4 REMARK 4 3S5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52281 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.66600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, 100MM SODIUM CHLORIDE, REMARK 280 50MM MAGNESIUM CHLORIDE, 100MM CACODYLATE, PH 6.1, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.30500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 HIS A 59 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 127 CG CD1 CD2 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 N4 DC B 267 CA XL3 B 1 1.48 REMARK 500 SG CYS A 169 SG XL3 B 1 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG C 279 O3' DG C 279 C3' -0.042 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 DC B 259 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT B 260 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 261 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 265 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 266 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 268 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 273 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT C 278 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DT C 278 N3 - C4 - O4 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT C 278 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG C 279 C3' - C2' - C1' ANGL. DEV. = -5.5 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 ARG A 110 151.09 173.54 REMARK 500 PHE A 124 -47.46 -133.02 REMARK 500 SER A 125 -106.45 -140.42 REMARK 500 SER A 125 -106.45 93.32 REMARK 500 ASP A 163 -169.34 -169.24 REMARK 500 ARG A 210 60.18 -107.41 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 A 1 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 171 NE2 REMARK 620 2 ASP A 173 OD1 99.4 REMARK 620 3 HIS A 236 NE2 90.4 100.9 REMARK 620 4 AKG A 259 O5 89.3 165.8 90.2 REMARK 620 5 AKG A 259 O2 90.4 91.2 167.6 77.5 REMARK 620 6 HOH A 265 O 177.4 82.9 90.4 88.2 88.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XL3 B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BTY RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH DIFFERENT DSDNA. REMARK 900 RELATED ID: 3S57 RELATED DB: PDB DBREF 3S5A A 56 258 UNP Q6NS38 ALKB2_HUMAN 56 258 DBREF 3S5A B 259 272 PDB 3S5A 3S5A 259 272 DBREF 3S5A C 271 284 PDB 3S5A 3S5A 271 284 SEQADV 3S5A MET A 55 UNP Q6NS38 EXPRESSION TAG SEQADV 3S5A SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3S5A SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3S5A CYS A 169 UNP Q6NS38 GLY 169 ENGINEERED MUTATION SEQADV 3S5A SER A 192 UNP Q6NS38 CYS 192 ENGINEERED MUTATION SEQRES 1 A 204 MET SER TRP ARG HIS ILE ARG ALA GLU GLY LEU ASP SER SEQRES 2 A 204 SER TYR THR VAL LEU PHE GLY LYS ALA GLU ALA ASP GLU SEQRES 3 A 204 ILE PHE GLN GLU LEU GLU LYS GLU VAL GLU TYR PHE THR SEQRES 4 A 204 GLY ALA LEU ALA ARG VAL GLN VAL PHE GLY LYS TRP HIS SEQRES 5 A 204 SER VAL PRO ARG LYS GLN ALA THR TYR GLY ASP ALA GLY SEQRES 6 A 204 LEU THR TYR THR PHE SER GLY LEU THR LEU SER PRO LYS SEQRES 7 A 204 PRO TRP ILE PRO VAL LEU GLU ARG ILE ARG ASP HIS VAL SEQRES 8 A 204 SER GLY VAL THR GLY GLN THR PHE ASN PHE VAL LEU ILE SEQRES 9 A 204 ASN ARG TYR LYS ASP GLY SER ASP HIS ILE CYS GLU HIS SEQRES 10 A 204 ARG ASP ASP GLU ARG GLU LEU ALA PRO GLY SER PRO ILE SEQRES 11 A 204 ALA SER VAL SER PHE GLY ALA SER ARG ASP PHE VAL PHE SEQRES 12 A 204 ARG HIS LYS ASP SER ARG GLY LYS SER PRO SER ARG ARG SEQRES 13 A 204 VAL ALA VAL VAL ARG LEU PRO LEU ALA HIS GLY SER LEU SEQRES 14 A 204 LEU MET MET ASN HIS PRO THR ASN THR HIS TRP TYR HIS SEQRES 15 A 204 SER LEU PRO VAL ARG LYS LYS VAL LEU ALA PRO ARG VAL SEQRES 16 A 204 ASN LEU THR PHE ARG LYS ILE LEU LEU SEQRES 1 B 14 DC DT DG DT DC DT DC DA DC DT DG DT DC SEQRES 2 B 14 DG SEQRES 1 C 14 DT DC DG DA DC DA DG DT DG DA DG DA DC SEQRES 2 C 14 DA HET MN A 1 1 HET AKG A 259 10 HET GOL A 260 6 HET GOL A 2 6 HET GOL A 3 6 HET XL3 B 1 4 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM GOL GLYCEROL HETNAM XL3 PROPANE-1-THIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 XL3 C3 H8 S FORMUL 10 HOH *338(H2 O) HELIX 1 1 GLY A 74 VAL A 89 1 16 HELIX 2 2 THR A 93 LEU A 96 5 4 HELIX 3 3 ILE A 135 GLY A 150 1 16 HELIX 4 4 ASP A 201 ARG A 203 5 3 HELIX 5 5 PRO A 229 HIS A 233 1 5 SHEET 1 A 8 ARG A 58 ALA A 62 0 SHEET 2 A 8 LEU A 65 VAL A 71 -1 O SER A 67 N ILE A 60 SHEET 3 A 8 SER A 222 MET A 226 -1 O LEU A 223 N THR A 70 SHEET 4 A 8 ILE A 184 GLY A 190 -1 N SER A 186 O LEU A 224 SHEET 5 A 8 ARG A 248 ARG A 254 -1 O LEU A 251 N VAL A 187 SHEET 6 A 8 PHE A 155 TYR A 161 -1 N ASN A 159 O ASN A 250 SHEET 7 A 8 LYS A 111 GLY A 116 -1 N ALA A 113 O ILE A 158 SHEET 8 A 8 LYS A 132 PRO A 133 1 O LYS A 132 N THR A 114 SHEET 1 B 2 ARG A 98 VAL A 101 0 SHEET 2 B 2 LYS A 104 SER A 107 -1 O LYS A 104 N VAL A 101 SHEET 1 C 2 TYR A 122 THR A 123 0 SHEET 2 C 2 THR A 128 LEU A 129 -1 O LEU A 129 N TYR A 122 SHEET 1 D 4 ILE A 168 HIS A 171 0 SHEET 2 D 4 TRP A 234 LEU A 238 -1 O HIS A 236 N HIS A 171 SHEET 3 D 4 ARG A 193 HIS A 199 -1 N ARG A 198 O TYR A 235 SHEET 4 D 4 VAL A 214 LEU A 218 -1 O VAL A 214 N PHE A 197 LINK MN MN A 1 NE2 HIS A 171 1555 1555 2.13 LINK MN MN A 1 OD1 ASP A 173 1555 1555 2.16 LINK MN MN A 1 NE2 HIS A 236 1555 1555 2.23 LINK MN MN A 1 O5 AKG A 259 1555 1555 2.20 LINK MN MN A 1 O2 AKG A 259 1555 1555 2.21 LINK MN MN A 1 O HOH A 265 1555 1555 2.25 CISPEP 1 HIS A 228 PRO A 229 0 2.56 CISPEP 2 HIS A 228 PRO A 229 0 1.43 SITE 1 AC1 5 HIS A 171 ASP A 173 HIS A 236 AKG A 259 SITE 2 AC1 5 HOH A 265 SITE 1 AC2 14 MN A 1 LEU A 157 ASN A 159 TYR A 161 SITE 2 AC2 14 ILE A 168 HIS A 171 ASP A 173 HIS A 236 SITE 3 AC2 14 ARG A 248 ASN A 250 ARG A 254 HOH A 265 SITE 4 AC2 14 HOH A 339 HOH A 370 SITE 1 AC3 8 HOH A 50 SER A 107 VAL A 108 ARG A 110 SITE 2 AC3 8 LYS A 162 ASP A 166 HOH A 267 HOH A 270 SITE 1 AC4 5 ARG A 58 HIS A 59 ILE A 60 ARG A 61 SITE 2 AC4 5 HOH A 378 SITE 1 AC5 6 VAL A 196 ARG A 215 PRO A 239 ARG A 241 SITE 2 AC5 6 HOH A 367 DA C 274 SITE 1 AC6 3 CYS A 169 DA B 266 DC B 267 CRYST1 45.968 60.610 65.588 90.00 90.52 90.00 P 1 21 1 2 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 0.021754 0.000000 0.000198 0.00000 SCALE2 0.000000 0.016499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015247 0.00000