HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 26-JUL-11 3T4H TITLE CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(III) AND N-OXALYL-S-(3- TITLE 2 NITROBENZYL)-L-CYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: B; 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 J.MA,W.S.AIK,M.A.MCDONOUGH,C.J.SCHOFIELD REVDAT 4 28-FEB-24 3T4H 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3T4H 1 REMARK REVDAT 2 21-MAR-12 3T4H 1 JRNL REVDAT 1 07-MAR-12 3T4H 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 22754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1124 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 21.1388 - 3.2964 0.97 2703 140 0.1535 0.1701 REMARK 3 2 3.2964 - 2.6180 1.00 2763 151 0.1535 0.1798 REMARK 3 3 2.6180 - 2.2875 1.00 2811 144 0.1605 0.1948 REMARK 3 4 2.2875 - 2.0786 1.00 2802 150 0.1619 0.1967 REMARK 3 5 2.0786 - 1.9297 0.99 2746 145 0.1563 0.2148 REMARK 3 6 1.9297 - 1.8160 0.97 2730 142 0.1636 0.1885 REMARK 3 7 1.8160 - 1.7251 0.93 2606 131 0.1758 0.2181 REMARK 3 8 1.7251 - 1.6500 0.88 2469 121 0.1983 0.2377 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 : 0.39 REMARK 3 B_SOL : 59.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.92150 REMARK 3 B22 (A**2) : -1.52830 REMARK 3 B33 (A**2) : -1.39320 REMARK 3 B12 (A**2) : 3.57700 REMARK 3 B13 (A**2) : 1.59390 REMARK 3 B23 (A**2) : -0.18780 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 1673 REMARK 3 ANGLE : 1.440 2280 REMARK 3 CHIRALITY : 0.092 237 REMARK 3 PLANARITY : 0.006 300 REMARK 3 DIHEDRAL : 15.541 628 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 13:65) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5041 -1.3566 -5.3402 REMARK 3 T TENSOR REMARK 3 T11: 0.0676 T22: 0.1194 REMARK 3 T33: 0.0932 T12: 0.0004 REMARK 3 T13: -0.0314 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.7365 L22: 4.7536 REMARK 3 L33: 1.8224 L12: 0.8324 REMARK 3 L13: 0.0129 L23: 0.2043 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: 0.0776 S13: -0.0706 REMARK 3 S21: -0.0823 S22: 0.0005 S23: -0.0097 REMARK 3 S31: 0.0916 S32: -0.0058 S33: 0.0124 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 66:106) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7372 -7.0071 -0.1879 REMARK 3 T TENSOR REMARK 3 T11: 0.0621 T22: 0.1150 REMARK 3 T33: 0.1638 T12: 0.0097 REMARK 3 T13: -0.0140 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 2.5547 L22: 5.1381 REMARK 3 L33: 2.0029 L12: 0.5009 REMARK 3 L13: 0.4083 L23: 0.4786 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: -0.1140 S13: -0.2251 REMARK 3 S21: 0.2893 S22: -0.0411 S23: -0.0678 REMARK 3 S31: 0.2047 S32: 0.0283 S33: -0.0162 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 107:214) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6683 3.6420 1.5725 REMARK 3 T TENSOR REMARK 3 T11: 0.1247 T22: 0.1079 REMARK 3 T33: 0.1102 T12: 0.0044 REMARK 3 T13: 0.0058 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.9986 L22: 2.0426 REMARK 3 L33: 2.2716 L12: 0.0685 REMARK 3 L13: 0.3296 L23: 0.3389 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: -0.1845 S13: -0.0193 REMARK 3 S21: 0.2428 S22: 0.0664 S23: -0.0016 REMARK 3 S31: 0.0372 S32: -0.0863 S33: -0.0444 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 3T4H 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_1000067025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : 24608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 21.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.22600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2M SODIUM CHLORIDE, REMARK 280 0.1M HEPES PH7.5, 2.2MM AMMONIUM IRON(II) SULFATE, 5.7MM N- REMARK 280 OXALYL-S-(3-NITROBENZYL)-L-CYSTEINE , VAPOR DIFFUSION, SITTING REMARK 280 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: 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 MET B 11 REMARK 465 GLN B 12 REMARK 465 GLU B 13 REMARK 465 LYS B 215 REMARK 465 GLU B 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 GLN B 101 OE1 NE2 REMARK 470 LYS B 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 OG1 THR B 71 O HOH B 391 1.98 REMARK 500 OE1 GLN B 155 O HOH B 390 2.09 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 B 391 O HOH B 400 1545 2.18 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 B 73 44.48 38.67 REMARK 500 ILE B 201 -74.48 68.72 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 B 300 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 131 NE2 REMARK 620 2 ASP B 133 OD1 91.4 REMARK 620 3 HIS B 187 NE2 89.5 91.5 REMARK 620 4 MD5 B 217 OAI 86.2 102.0 165.9 REMARK 620 5 MD5 B 217 OAH 98.4 170.1 89.3 78.1 REMARK 620 6 HOH B 386 O 172.4 90.1 97.8 86.2 80.1 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 B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MD5 B 217 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: 3T3Y RELATED DB: PDB REMARK 900 RELATED ID: 3T4V RELATED DB: PDB DBREF 3T4H B 12 216 UNP P05050 ALKB_ECOLI 12 216 SEQADV 3T4H MET B 11 UNP P05050 EXPRESSION TAG SEQRES 1 B 206 MET GLN GLU PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG SEQRES 2 B 206 ARG PHE ALA PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP SEQRES 3 B 206 ILE ASN ASP VAL ALA SER GLN SER PRO PHE ARG GLN MET SEQRES 4 B 206 VAL THR PRO GLY GLY TYR THR MET SER VAL ALA MET THR SEQRES 5 B 206 ASN CYS GLY HIS LEU GLY TRP THR THR HIS ARG GLN GLY SEQRES 6 B 206 TYR LEU TYR SER PRO ILE ASP PRO GLN THR ASN LYS PRO SEQRES 7 B 206 TRP PRO ALA MET PRO GLN SER PHE HIS ASN LEU CYS GLN SEQRES 8 B 206 ARG ALA ALA THR ALA ALA GLY TYR PRO ASP PHE GLN PRO SEQRES 9 B 206 ASP ALA CYS LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS SEQRES 10 B 206 LEU SER LEU HIS GLN ASP LYS ASP GLU PRO ASP LEU ARG SEQRES 11 B 206 ALA PRO ILE VAL SER VAL SER LEU GLY LEU PRO ALA ILE SEQRES 12 B 206 PHE GLN PHE GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS SEQRES 13 B 206 ARG LEU LEU LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY SEQRES 14 B 206 GLY GLU SER ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU SEQRES 15 B 206 LYS ALA GLY PHE HIS PRO LEU THR ILE ASP CYS ARG TYR SEQRES 16 B 206 ASN LEU THR PHE ARG GLN ALA GLY LYS LYS GLU HET FE B 300 1 HET EPE B 1 15 HET MD5 B 217 22 HETNAM FE FE (III) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM MD5 N-(CARBOXYCARBONYL)-S-(3-NITROBENZYL)-L-CYSTEINE HETSYN EPE HEPES FORMUL 2 FE FE 3+ FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 MD5 C12 H12 N2 O7 S FORMUL 5 HOH *192(H2 O) HELIX 1 1 ALA B 29 SER B 44 1 16 HELIX 2 2 PRO B 93 ALA B 107 1 15 HELIX 3 3 GLY B 180 PHE B 185 5 6 SHEET 1 A 6 ALA B 19 LEU B 22 0 SHEET 2 A 6 VAL B 175 TRP B 178 -1 O VAL B 175 N LEU B 22 SHEET 3 A 6 ILE B 143 GLY B 149 -1 N SER B 145 O VAL B 176 SHEET 4 A 6 ARG B 204 PHE B 209 -1 O PHE B 209 N VAL B 144 SHEET 5 A 6 ALA B 116 TYR B 122 -1 N TYR B 122 O ARG B 204 SHEET 6 A 6 ALA B 60 GLY B 65 -1 N ALA B 60 O ARG B 121 SHEET 1 B 2 GLY B 68 HIS B 72 0 SHEET 2 B 2 GLY B 75 SER B 79 -1 O LEU B 77 N THR B 70 SHEET 1 C 4 LEU B 128 HIS B 131 0 SHEET 2 C 4 HIS B 187 ILE B 189 -1 O HIS B 187 N HIS B 131 SHEET 3 C 4 ALA B 152 PHE B 156 -1 N GLN B 155 O GLY B 188 SHEET 4 C 4 LYS B 166 LEU B 170 -1 O LEU B 168 N PHE B 154 LINK NE2 HIS B 131 FE FE B 300 1555 1555 2.18 LINK OD1 ASP B 133 FE FE B 300 1555 1555 2.13 LINK NE2 HIS B 187 FE FE B 300 1555 1555 2.15 LINK OAI MD5 B 217 FE FE B 300 1555 1555 2.17 LINK OAH MD5 B 217 FE FE B 300 1555 1555 2.18 LINK FE FE B 300 O HOH B 386 1555 1555 2.44 SITE 1 AC1 5 HIS B 131 ASP B 133 HIS B 187 MD5 B 217 SITE 2 AC1 5 HOH B 386 SITE 1 AC2 13 MET B 57 MET B 61 TRP B 69 LEU B 118 SITE 2 AC2 13 LEU B 128 SER B 129 HIS B 131 ASP B 133 SITE 3 AC2 13 ARG B 210 MD5 B 217 HOH B 232 HOH B 302 SITE 4 AC2 13 HOH B 303 SITE 1 AC3 22 EPE B 1 LEU B 118 ASN B 120 TYR B 122 SITE 2 AC3 22 LEU B 128 HIS B 131 ASP B 133 SER B 145 SITE 3 AC3 22 PHE B 154 PHE B 156 TRP B 178 SER B 182 SITE 4 AC3 22 PHE B 185 HIS B 187 ILE B 189 ARG B 204 SITE 5 AC3 22 ASN B 206 THR B 208 ARG B 210 FE B 300 SITE 6 AC3 22 HOH B 366 HOH B 386 CRYST1 36.661 38.830 40.274 77.64 75.44 66.42 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 0.027277 -0.011903 -0.005610 0.00000 SCALE2 0.000000 0.028099 -0.003622 0.00000 SCALE3 0.000000 0.000000 0.025866 0.00000