HEADER OXIDOREDUCTASE/DNA 06-NOV-13 4NII TITLE CRYSTAL STRUCTURE OF ALKB D135I MUTANT PROTEIN WITH COFACTORS BOUND TO TITLE 2 DSDNA CONTAINING M6A/A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 12-215; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB, DNA OXIDATIVE DEMETHYLASE COMPND 6 ALKB; COMPND 7 EC: 1.14.11.33; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'; COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ALKB, AIDD, B2212, JW2200; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS DNA/RNA DIRECT REPAIR, JELLY-ROLL FOLD, DNA/RNA DEMETHYLATION REPAIR, KEYWDS 2 FE(II), 2-KG, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.Q.YI,C.X.ZHU REVDAT 3 20-SEP-23 4NII 1 REMARK SEQADV LINK REVDAT 2 28-MAY-14 4NII 1 ATOM HET HETATM HETNAM REVDAT 2 2 1 LINK REVDAT 1 16-APR-14 4NII 0 JRNL AUTH C.ZHU,C.YI JRNL TITL SWITCHING DEMETHYLATION ACTIVITIES BETWEEN ALKB FAMILY JRNL TITL 2 RNA/DNA DEMETHYLASES THROUGH EXCHANGE OF ACTIVE-SITE JRNL TITL 3 RESIDUES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 3659 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 24596302 JRNL DOI 10.1002/ANIE.201310050 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 36703 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1939 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2671 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1554 REMARK 3 NUCLEIC ACID ATOMS : 506 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.62000 REMARK 3 B22 (A**2) : -1.34000 REMARK 3 B33 (A**2) : 2.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.072 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2263 ; 0.012 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 1901 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3184 ; 1.538 ; 1.764 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4380 ; 0.998 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 216 ; 6.545 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;36.345 ;22.368 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 263 ;11.728 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.237 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 317 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2288 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 550 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : 3 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 213 REMARK 3 ORIGIN FOR THE GROUP (A): 23.0190 1.8796 75.4353 REMARK 3 T TENSOR REMARK 3 T11: 0.0259 T22: 0.0266 REMARK 3 T33: 0.0023 T12: -0.0017 REMARK 3 T13: 0.0036 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.1604 L22: 0.1963 REMARK 3 L33: 0.0440 L12: 0.0147 REMARK 3 L13: -0.0271 L23: 0.0812 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: -0.0010 S13: 0.0137 REMARK 3 S21: -0.0083 S22: 0.0015 S23: 0.0007 REMARK 3 S31: 0.0036 S32: 0.0048 S33: -0.0015 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 5 REMARK 3 RESIDUE RANGE : C 10 C 13 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9757 -7.4508 50.8852 REMARK 3 T TENSOR REMARK 3 T11: 0.0266 T22: 0.0508 REMARK 3 T33: 0.0204 T12: 0.0121 REMARK 3 T13: 0.0071 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.4252 L22: 2.6938 REMARK 3 L33: 2.4568 L12: 0.6072 REMARK 3 L13: 0.5782 L23: 0.9871 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: 0.1583 S13: -0.1073 REMARK 3 S21: -0.0573 S22: 0.1139 S23: 0.0228 REMARK 3 S31: -0.1709 S32: 0.1378 S33: -0.1446 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 13 REMARK 3 RESIDUE RANGE : C 1 C 9 REMARK 3 ORIGIN FOR THE GROUP (A): 28.1412 -15.9236 62.9611 REMARK 3 T TENSOR REMARK 3 T11: 0.0274 T22: 0.0284 REMARK 3 T33: 0.0109 T12: 0.0053 REMARK 3 T13: 0.0024 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.4881 L22: 0.2143 REMARK 3 L33: 0.0324 L12: -0.3030 REMARK 3 L13: -0.1157 L23: 0.0668 REMARK 3 S TENSOR REMARK 3 S11: 0.0246 S12: 0.0327 S13: -0.0260 REMARK 3 S21: -0.0069 S22: -0.0263 S23: 0.0069 REMARK 3 S31: -0.0144 S32: -0.0038 S33: 0.0017 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 4NII COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 6.5 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) : 0.97 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.622 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: REFMAC 5.7.0029 REMARK 200 STARTING MODEL: PDB ENTRY 3BIE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 0.1 M SODIUM CHLORIDE, REMARK 280 0.05 M MAGNESIUM CHLORIDE, 0.1 M CACODYLATE, PH 6.5, 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 37.95100 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: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 GLU A 136 REMARK 465 PRO A 137 REMARK 465 ASP A 138 REMARK 465 LYS A 215 REMARK 465 GLU A 216 REMARK 465 DT B 1 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 13 CG CD OE1 OE2 REMARK 470 ILE A 135 CG1 CG2 CD1 REMARK 470 DT C 8 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 8 C7 C6 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 OD1 ASN A 120 O HOH A 527 2.07 REMARK 500 O HOH A 494 O HOH A 617 2.10 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 O HOH A 541 O HOH B 206 2758 1.77 REMARK 500 NE2 GLN A 101 O HOH A 521 2758 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = 3.1 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 HIS A 72 -165.28 -164.67 REMARK 500 ARG A 140 61.29 -119.09 REMARK 500 ILE A 201 -70.73 67.77 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 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 NE2 REMARK 620 2 ASP A 133 OD1 94.9 REMARK 620 3 HIS A 187 NE2 92.8 91.4 REMARK 620 4 AKG A 302 O1 97.5 107.8 157.2 REMARK 620 5 AKG A 302 O5 93.9 171.2 88.4 70.7 REMARK 620 6 HOH A 449 O 176.6 87.5 84.7 84.0 83.7 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NID RELATED DB: PDB REMARK 900 RELATED ID: 4NIG RELATED DB: PDB REMARK 900 RELATED ID: 4NIH RELATED DB: PDB DBREF 4NII A 12 216 UNP P05050 ALKB_ECOLI 12 216 DBREF 4NII B 1 13 PDB 4NII 4NII 1 13 DBREF 4NII C 1 13 PDB 4NII 4NII 1 13 SEQADV 4NII CYS A 129 UNP P05050 SER 129 ENGINEERED MUTATION SEQADV 4NII ILE A 135 UNP P05050 ASP 135 ENGINEERED MUTATION SEQRES 1 A 205 GLN GLU PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG ARG SEQRES 2 A 205 PHE ALA PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP ILE SEQRES 3 A 205 ASN ASP VAL ALA SER GLN SER PRO PHE ARG GLN MET VAL SEQRES 4 A 205 THR PRO GLY GLY TYR THR MET SER VAL ALA MET THR ASN SEQRES 5 A 205 CYS GLY HIS LEU GLY TRP THR THR HIS ARG GLN GLY TYR SEQRES 6 A 205 LEU TYR SER PRO ILE ASP PRO GLN THR ASN LYS PRO TRP SEQRES 7 A 205 PRO ALA MET PRO GLN SER PHE HIS ASN LEU CYS GLN ARG SEQRES 8 A 205 ALA ALA THR ALA ALA GLY TYR PRO ASP PHE GLN PRO ASP SEQRES 9 A 205 ALA CYS LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS LEU SEQRES 10 A 205 CYS LEU HIS GLN ASP LYS ILE GLU PRO ASP LEU ARG ALA SEQRES 11 A 205 PRO ILE VAL SER VAL SER LEU GLY LEU PRO ALA ILE PHE SEQRES 12 A 205 GLN PHE GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS ARG SEQRES 13 A 205 LEU LEU LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY GLY SEQRES 14 A 205 GLU SER ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU LYS SEQRES 15 A 205 ALA GLY PHE HIS PRO LEU THR ILE ASP CYS ARG TYR ASN SEQRES 16 A 205 LEU THR PHE ARG GLN ALA GLY LYS LYS GLU SEQRES 1 B 13 DT DA DG DG DT DA DA 6MA DA 2YR DC DG DT SEQRES 1 C 13 DA DA DC DG DG DT DA DT DT DA DC DC DT MODRES 4NII 6MA B 8 A HET 6MA B 8 22 HET 2YR B 10 22 HET MN A 301 1 HET AKG A 302 10 HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 6MA C11 H16 N5 O6 P FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 HOH *328(H2 O) HELIX 1 1 ALA A 29 SER A 44 1 16 HELIX 2 2 PRO A 93 ALA A 107 1 15 HELIX 3 3 GLY A 179 ARG A 183 5 5 SHEET 1 A 7 GLU A 13 ALA A 16 0 SHEET 2 A 7 ALA A 19 LEU A 22 -1 O ILE A 21 N GLU A 13 SHEET 3 A 7 VAL A 175 TRP A 178 -1 O VAL A 175 N LEU A 22 SHEET 4 A 7 ILE A 143 GLY A 149 -1 N ILE A 143 O TRP A 178 SHEET 5 A 7 ARG A 204 ARG A 210 -1 O PHE A 209 N VAL A 144 SHEET 6 A 7 ALA A 116 TYR A 122 -1 N TYR A 122 O ARG A 204 SHEET 7 A 7 ALA A 60 CYS A 64 -1 N ALA A 60 O ARG A 121 SHEET 1 B 2 GLY A 68 HIS A 72 0 SHEET 2 B 2 GLY A 75 SER A 79 -1 O LEU A 77 N THR A 70 SHEET 1 C 2 ILE A 81 ASP A 82 0 SHEET 2 C 2 LYS A 87 PRO A 88 -1 O LYS A 87 N ASP A 82 SHEET 1 D 4 LEU A 128 HIS A 131 0 SHEET 2 D 4 HIS A 187 ILE A 189 -1 O ILE A 189 N LEU A 128 SHEET 3 D 4 ALA A 152 PHE A 156 -1 N GLN A 155 O GLY A 188 SHEET 4 D 4 LYS A 166 LEU A 170 -1 O LEU A 170 N ALA A 152 LINK SG CYS A 129 S 2YR B 10 1555 1555 2.13 LINK O3' DA B 7 P 6MA B 8 1555 1555 1.57 LINK O3' 6MA B 8 P DA B 9 1555 1555 1.62 LINK O3' DA B 9 P 2YR B 10 1555 1555 1.60 LINK O3' 2YR B 10 P DC B 11 1555 1555 1.60 LINK NE2 HIS A 131 MN MN A 301 1555 1555 2.24 LINK OD1 ASP A 133 MN MN A 301 1555 1555 2.18 LINK NE2 HIS A 187 MN MN A 301 1555 1555 2.26 LINK MN MN A 301 O1 AKG A 302 1555 1555 2.20 LINK MN MN A 301 O5 AKG A 302 1555 1555 2.39 LINK MN MN A 301 O HOH A 449 1555 1555 2.38 SITE 1 AC1 5 HIS A 131 ASP A 133 HIS A 187 AKG A 302 SITE 2 AC1 5 HOH A 449 SITE 1 AC2 17 LEU A 118 ASN A 120 TYR A 122 LEU A 128 SITE 2 AC2 17 HIS A 131 ASP A 133 HIS A 187 ILE A 189 SITE 3 AC2 17 ARG A 204 ASN A 206 THR A 208 MN A 301 SITE 4 AC2 17 HOH A 409 HOH A 415 HOH A 449 HOH A 452 SITE 5 AC2 17 6MA B 8 CRYST1 41.374 75.902 52.285 90.00 108.60 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 0.024170 0.000000 0.008134 0.00000 SCALE2 0.000000 0.013175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020180 0.00000