HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 25-JUL-11 3T3Y TITLE CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(III) AND 2-(3- TITLE 2 HYDROXYPICOLINOMIDO)ACETIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 12-216; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: AIDD, ALKB, B2212, JW2200; 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: PET24A KEYWDS DOUBLE-STRANDED BETA-HELIX, NUCLEIC ACID DEMETHYLASE, OXIDOREDUCTASE- KEYWDS 2 OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.S.AIK,M.A.MCDONOUGH,C.J.SCHOFIELD REVDAT 4 13-SEP-23 3T3Y 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3T3Y 1 REMARK REVDAT 2 21-MAR-12 3T3Y 1 JRNL REVDAT 1 07-MAR-12 3T3Y 0 JRNL AUTH E.C.WOON,M.DEMETRIADES,E.A.BAGG,W.AIK,S.M.KRYLOVA,J.H.MA, JRNL AUTH 2 M.CHAN,L.J.WALPORT,D.W.WEGMAN,K.N.DACK,M.A.MCDONOUGH, JRNL AUTH 3 S.N.KRYLOV,C.J.SCHOFIELD JRNL TITL DYNAMIC COMBINATORIAL MASS SPECTROMETRY LEADS TO INHIBITORS JRNL TITL 2 OF A 2-OXOGLUTARATE-DEPENDENT NUCLEIC ACID DEMETHYLASE. JRNL REF J.MED.CHEM. V. 55 2173 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22263962 JRNL DOI 10.1021/JM201417E REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.9143 - 3.4191 1.00 2418 130 0.1674 0.1893 REMARK 3 2 3.4191 - 2.7152 1.00 2425 131 0.1803 0.2200 REMARK 3 3 2.7152 - 2.3724 1.00 2433 128 0.2046 0.2847 REMARK 3 4 2.3724 - 2.1557 0.99 2393 121 0.1891 0.2327 REMARK 3 5 2.1557 - 2.0013 0.98 2379 129 0.2179 0.2895 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 46.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.77990 REMARK 3 B22 (A**2) : 0.15620 REMARK 3 B33 (A**2) : 2.62370 REMARK 3 B12 (A**2) : 5.52950 REMARK 3 B13 (A**2) : 0.30400 REMARK 3 B23 (A**2) : -4.13630 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1588 REMARK 3 ANGLE : 1.254 2174 REMARK 3 CHIRALITY : 0.068 227 REMARK 3 PLANARITY : 0.004 292 REMARK 3 DIHEDRAL : 14.684 574 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 16:65) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5899 -1.9663 -6.1961 REMARK 3 T TENSOR REMARK 3 T11: 0.2076 T22: 0.1989 REMARK 3 T33: 0.1991 T12: -0.0178 REMARK 3 T13: 0.0658 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 3.4774 L22: 3.4013 REMARK 3 L33: 1.5860 L12: -1.1519 REMARK 3 L13: 1.1404 L23: 1.5355 REMARK 3 S TENSOR REMARK 3 S11: 0.1603 S12: 0.1495 S13: -0.2193 REMARK 3 S21: -0.0878 S22: -0.2561 S23: 0.3401 REMARK 3 S31: 0.0935 S32: -0.1128 S33: -0.0383 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 66:79) REMARK 3 ORIGIN FOR THE GROUP (A): 3.5766 -11.6997 5.6565 REMARK 3 T TENSOR REMARK 3 T11: 0.5222 T22: 0.5133 REMARK 3 T33: 0.4772 T12: 0.1231 REMARK 3 T13: 0.2132 T23: 0.1868 REMARK 3 L TENSOR REMARK 3 L11: 4.0431 L22: 2.7062 REMARK 3 L33: 2.9126 L12: 3.2988 REMARK 3 L13: -0.7669 L23: -0.4266 REMARK 3 S TENSOR REMARK 3 S11: -0.3988 S12: -0.8418 S13: -1.1618 REMARK 3 S21: 0.6854 S22: 0.1748 S23: 0.4521 REMARK 3 S31: 0.6502 S32: -0.6464 S33: 0.2669 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 80:122) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9112 -1.8198 -2.2628 REMARK 3 T TENSOR REMARK 3 T11: 0.1027 T22: 0.1774 REMARK 3 T33: 0.3070 T12: 0.0011 REMARK 3 T13: -0.0108 T23: -0.0424 REMARK 3 L TENSOR REMARK 3 L11: 2.7374 L22: 2.5663 REMARK 3 L33: 1.8764 L12: -1.1053 REMARK 3 L13: -0.9407 L23: -0.0825 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: -0.2883 S13: 0.2948 REMARK 3 S21: 0.0576 S22: 0.0930 S23: -0.5051 REMARK 3 S31: -0.0037 S32: 0.3039 S33: -0.0206 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 123:214) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4551 4.1007 0.9721 REMARK 3 T TENSOR REMARK 3 T11: 0.1662 T22: 0.1900 REMARK 3 T33: 0.1112 T12: 0.0194 REMARK 3 T13: -0.0133 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 3.9792 L22: 3.9477 REMARK 3 L33: 1.0816 L12: -1.6225 REMARK 3 L13: -1.1108 L23: 0.2572 REMARK 3 S TENSOR REMARK 3 S11: -0.1460 S12: -0.3400 S13: -0.2360 REMARK 3 S21: 0.3809 S22: 0.2162 S23: 0.1937 REMARK 3 S31: 0.0205 S32: 0.0937 S33: -0.0634 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3T3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5412 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12688 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.307 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: 3T4H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M BIS-TRIS PH6.5, REMARK 280 0.44MM AMMONIUM IRON(II) SULPHATE, 1MM 2-(3-HYDROXYPICOLINOMIDO) REMARK 280 ACETIC ACID, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 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 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 MET A 11 REMARK 465 GLN A 12 REMARK 465 GLU A 13 REMARK 465 PRO A 14 REMARK 465 LEU A 15 REMARK 465 LYS A 215 REMARK 465 GLU A 216 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 TYR A 55 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 55 OH REMARK 470 ARG A 73 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 74 CB CG CD OE1 NE2 REMARK 470 LYS A 127 CE NZ REMARK 470 LYS A 134 CE NZ REMARK 470 ASP A 135 CG OD1 OD2 REMARK 470 ARG A 140 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 160 CB CG CD CE NZ REMARK 470 ARG A 161 CB CG CD NE CZ NH1 NH2 REMARK 470 LEU A 184 CB CG CD1 CD2 REMARK 470 LYS A 214 CG CD CE NZ 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 HOH A 230 O HOH A 260 2.17 REMARK 500 OE1 GLN A 94 O HOH A 292 2.17 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 ILE A 201 -96.72 69.47 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 FE A 300 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 1 O REMARK 620 2 HIS A 131 NE2 93.6 REMARK 620 3 ASP A 133 OD1 87.8 94.0 REMARK 620 4 HIS A 187 NE2 174.0 89.6 87.0 REMARK 620 5 MD6 A 401 N2 103.1 161.3 94.9 74.5 REMARK 620 6 MD6 A 401 O3 84.5 99.9 164.6 99.9 74.0 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 FE A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MD6 A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTARATE, REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEA-T REMARK 900 RELATED ID: 2FDF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH CO(II), 2-OXOGLUTARATE, REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEA-T REMARK 900 RELATED ID: 2FDG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), SUCCINATE, AND REMARK 900 METHYLATED TRINUCLEOTIDE T-MEA-T REMARK 900 RELATED ID: 2FDH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II), 2-OXOGLUTARATE, REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEA-T REMARK 900 RELATED ID: 2FDI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTARATE, REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEA-T (AIR 3 HOURS) REMARK 900 RELATED ID: 2FDJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II) AND SUCCINATE REMARK 900 RELATED ID: 2FDK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTARATE, REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEA-T (AIR 9 DAYS) REMARK 900 RELATED ID: 3BI3 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF ALKB PROTEIN BOUND TO DSDNA CONTAINING 1MEA/A REMARK 900 WITH COFACTORS REMARK 900 RELATED ID: 3BIE RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF E COLI ALKB BOUND TO DSDNA CONTAINING 1MEA/T REMARK 900 WITH MN AND 2KG REMARK 900 RELATED ID: 3BKZ RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF E COLI ALKB CROSSLINKED TO DSDNA IN THE ACTIVE REMARK 900 SITE REMARK 900 RELATED ID: 3H8O RELATED DB: PDB REMARK 900 STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3- REMARK 900 MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM REMARK 900 RELATED ID: 3H8R RELATED DB: PDB REMARK 900 STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3- REMARK 900 MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM REMARK 900 RELATED ID: 3H8X RELATED DB: PDB REMARK 900 STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3- REMARK 900 MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM REMARK 900 RELATED ID: 3I2O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTARATE REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEA-T REMARK 900 RELATED ID: 3I3M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II), 2-OXOGLUTARATE REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEC-T REMARK 900 RELATED ID: 3I3Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II) AND 2-OXOGLUTARATE REMARK 900 RELATED ID: 3I49 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2-OXOGLUTARATE REMARK 900 AND METHYLATED TRINUCLEOTIDE T-MEC-T REMARK 900 RELATED ID: 3KHB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI ALKB WITH CO(II) AND 2-OG REMARK 900 RELATED ID: 3KHC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI ALKB IN COMPLEX WITH SSDNA REMARK 900 CONTAINING A 1-METHYLGUANINE LESION REMARK 900 RELATED ID: 3O1M RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1O RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1P RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1R RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1S RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1T RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1U RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3O1V RELATED DB: PDB REMARK 900 IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR REMARK 900 DIOXYGENASE REMARK 900 RELATED ID: 3T4H RELATED DB: PDB REMARK 900 RELATED ID: 3T4V RELATED DB: PDB DBREF 3T3Y A 12 216 UNP P05050 ALKB_ECOLI 12 216 SEQADV 3T3Y MET A 11 UNP P05050 EXPRESSION TAG SEQRES 1 A 206 MET GLN GLU PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG SEQRES 2 A 206 ARG PHE ALA PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP SEQRES 3 A 206 ILE ASN ASP VAL ALA SER GLN SER PRO PHE ARG GLN MET SEQRES 4 A 206 VAL THR PRO GLY GLY TYR THR MET SER VAL ALA MET THR SEQRES 5 A 206 ASN CYS GLY HIS LEU GLY TRP THR THR HIS ARG GLN GLY SEQRES 6 A 206 TYR LEU TYR SER PRO ILE ASP PRO GLN THR ASN LYS PRO SEQRES 7 A 206 TRP PRO ALA MET PRO GLN SER PHE HIS ASN LEU CYS GLN SEQRES 8 A 206 ARG ALA ALA THR ALA ALA GLY TYR PRO ASP PHE GLN PRO SEQRES 9 A 206 ASP ALA CYS LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS SEQRES 10 A 206 LEU SER LEU HIS GLN ASP LYS ASP GLU PRO ASP LEU ARG SEQRES 11 A 206 ALA PRO ILE VAL SER VAL SER LEU GLY LEU PRO ALA ILE SEQRES 12 A 206 PHE GLN PHE GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS SEQRES 13 A 206 ARG LEU LEU LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY SEQRES 14 A 206 GLY GLU SER ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU SEQRES 15 A 206 LYS ALA GLY PHE HIS PRO LEU THR ILE ASP CYS ARG TYR SEQRES 16 A 206 ASN LEU THR PHE ARG GLN ALA GLY LYS LYS GLU HET FE A 300 1 HET MD6 A 401 14 HETNAM FE FE (III) ION HETNAM MD6 N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE FORMUL 2 FE FE 3+ FORMUL 3 MD6 C8 H8 N2 O4 FORMUL 4 HOH *85(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 180 PHE A 185 5 6 SHEET 1 A 6 ALA A 19 LEU A 22 0 SHEET 2 A 6 VAL A 175 TRP A 178 -1 O VAL A 175 N LEU A 22 SHEET 3 A 6 ILE A 143 GLY A 149 -1 N ILE A 143 O TRP A 178 SHEET 4 A 6 ARG A 204 ARG A 210 -1 O PHE A 209 N VAL A 144 SHEET 5 A 6 ALA A 116 TYR A 122 -1 N TYR A 122 O ARG A 204 SHEET 6 A 6 ALA A 60 CYS A 64 -1 N THR A 62 O ILE A 119 SHEET 1 B 2 GLY A 68 THR A 71 0 SHEET 2 B 2 TYR A 76 SER A 79 -1 O SER A 79 N GLY A 68 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 O HOH A 1 FE FE A 300 1555 1555 2.26 LINK NE2 HIS A 131 FE FE A 300 1555 1555 2.30 LINK OD1 ASP A 133 FE FE A 300 1555 1555 2.13 LINK NE2 HIS A 187 FE FE A 300 1555 1555 2.26 LINK FE FE A 300 N2 MD6 A 401 1555 1555 2.24 LINK FE FE A 300 O3 MD6 A 401 1555 1555 2.25 SITE 1 AC1 5 HOH A 1 HIS A 131 ASP A 133 HIS A 187 SITE 2 AC1 5 MD6 A 401 SITE 1 AC2 15 HOH A 1 HOH A 2 TYR A 122 LEU A 128 SITE 2 AC2 15 HIS A 131 ASP A 133 ILE A 143 SER A 145 SITE 3 AC2 15 TRP A 178 HIS A 187 ILE A 189 ARG A 204 SITE 4 AC2 15 ASN A 206 HOH A 281 FE A 300 CRYST1 36.813 38.594 40.487 71.25 72.21 66.70 P 1 1 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 0.027164 -0.011701 -0.006197 0.00000 SCALE2 0.000000 0.028212 -0.006649 0.00000 SCALE3 0.000000 0.000000 0.026650 0.00000