HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 26-JUL-11 3T4V TITLE CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(III) AND N-OXALYL-S-(2- TITLE 2 NAPTHALENEMETHYL)-L-CYSTEINE 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 3T4V 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3T4V 1 REMARK REVDAT 2 21-MAR-12 3T4V 1 JRNL REVDAT 1 07-MAR-12 3T4V 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. 1.73 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 19227 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1889 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 22.9965 - 4.0665 0.92 1307 143 0.1639 0.1654 REMARK 3 2 4.0665 - 3.2306 0.88 1240 136 0.1445 0.1851 REMARK 3 3 3.2306 - 2.8230 0.96 1358 150 0.1516 0.2103 REMARK 3 4 2.8230 - 2.5653 0.98 1387 156 0.1526 0.2231 REMARK 3 5 2.5653 - 2.3816 0.98 1393 149 0.1560 0.2068 REMARK 3 6 2.3816 - 2.2413 0.97 1365 145 0.1565 0.1839 REMARK 3 7 2.2413 - 2.1292 0.97 1384 160 0.1507 0.2170 REMARK 3 8 2.1292 - 2.0365 0.99 1378 149 0.1617 0.2355 REMARK 3 9 2.0365 - 1.9582 0.98 1385 145 0.1783 0.2079 REMARK 3 10 1.9582 - 1.8906 0.96 1365 158 0.1864 0.2510 REMARK 3 11 1.8906 - 1.8316 0.91 1303 126 0.2011 0.2661 REMARK 3 12 1.8316 - 1.7792 0.89 1272 131 0.2166 0.2425 REMARK 3 13 1.7792 - 1.7324 0.85 1201 141 0.2098 0.2612 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 61.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.85220 REMARK 3 B22 (A**2) : -0.37670 REMARK 3 B33 (A**2) : 2.22890 REMARK 3 B12 (A**2) : 2.52710 REMARK 3 B13 (A**2) : -2.40130 REMARK 3 B23 (A**2) : -5.21690 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 : 0.011 1644 REMARK 3 ANGLE : 1.486 2240 REMARK 3 CHIRALITY : 0.112 234 REMARK 3 PLANARITY : 0.009 294 REMARK 3 DIHEDRAL : 14.023 600 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 15:29) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8715 13.5894 -3.5742 REMARK 3 T TENSOR REMARK 3 T11: 0.1599 T22: 0.1634 REMARK 3 T33: 0.2298 T12: -0.0043 REMARK 3 T13: -0.0202 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 2.6615 L22: 4.4976 REMARK 3 L33: 4.1665 L12: -0.0844 REMARK 3 L13: -1.7514 L23: 2.3277 REMARK 3 S TENSOR REMARK 3 S11: -0.0476 S12: 0.1627 S13: 0.2339 REMARK 3 S21: -0.3025 S22: -0.1469 S23: 0.1349 REMARK 3 S31: -0.8776 S32: 0.0554 S33: 0.0460 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 30:59) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0035 -8.3605 -6.7394 REMARK 3 T TENSOR REMARK 3 T11: 0.1193 T22: 0.1001 REMARK 3 T33: 0.1048 T12: 0.0209 REMARK 3 T13: -0.0712 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 5.9208 L22: 5.4805 REMARK 3 L33: 3.0792 L12: 2.3902 REMARK 3 L13: -1.5922 L23: -0.8431 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.0521 S13: -0.2483 REMARK 3 S21: 0.0114 S22: -0.0382 S23: -0.0729 REMARK 3 S31: 0.1719 S32: 0.1088 S33: 0.0338 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 60:79) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4771 -11.6923 3.7637 REMARK 3 T TENSOR REMARK 3 T11: 0.1610 T22: 0.1666 REMARK 3 T33: 0.1939 T12: 0.0011 REMARK 3 T13: -0.0086 T23: -0.0319 REMARK 3 L TENSOR REMARK 3 L11: 3.1157 L22: 6.6109 REMARK 3 L33: 7.8364 L12: -0.8937 REMARK 3 L13: 0.8395 L23: -2.0180 REMARK 3 S TENSOR REMARK 3 S11: -0.0522 S12: -0.4095 S13: -0.2013 REMARK 3 S21: 0.4015 S22: 0.0398 S23: 0.0190 REMARK 3 S31: 0.3041 S32: -0.4192 S33: 0.0012 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 80:93) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6535 -13.5850 -3.4240 REMARK 3 T TENSOR REMARK 3 T11: 0.1663 T22: 0.1540 REMARK 3 T33: 0.2733 T12: 0.0230 REMARK 3 T13: 0.0136 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 3.4737 L22: 4.9475 REMARK 3 L33: 3.1411 L12: 3.6477 REMARK 3 L13: -2.0155 L23: -3.4535 REMARK 3 S TENSOR REMARK 3 S11: -0.0372 S12: 0.0346 S13: -0.0661 REMARK 3 S21: 0.1097 S22: -0.0112 S23: -0.0155 REMARK 3 S31: 0.0177 S32: -0.0625 S33: 0.0482 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 94:106) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6653 6.4860 -4.1917 REMARK 3 T TENSOR REMARK 3 T11: 0.1900 T22: 0.2311 REMARK 3 T33: 0.2714 T12: -0.0048 REMARK 3 T13: 0.0157 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 1.0376 L22: 2.0800 REMARK 3 L33: 2.0928 L12: -1.4362 REMARK 3 L13: -1.4629 L23: 2.0780 REMARK 3 S TENSOR REMARK 3 S11: -0.0199 S12: 0.0747 S13: 0.1939 REMARK 3 S21: -0.1846 S22: 0.3317 S23: -0.6838 REMARK 3 S31: -0.2164 S32: 0.3352 S33: -0.3109 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 107:122) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9070 1.4228 0.9144 REMARK 3 T TENSOR REMARK 3 T11: 0.1690 T22: 0.1612 REMARK 3 T33: 0.1867 T12: 0.0154 REMARK 3 T13: 0.0148 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 3.2163 L22: 6.1899 REMARK 3 L33: 2.9207 L12: 2.4426 REMARK 3 L13: 2.2696 L23: 3.1467 REMARK 3 S TENSOR REMARK 3 S11: 0.0821 S12: 0.0457 S13: -0.0843 REMARK 3 S21: 0.2395 S22: 0.1445 S23: -0.4659 REMARK 3 S31: 0.0794 S32: 0.2190 S33: -0.2623 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 123:142) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9662 -0.7464 7.3957 REMARK 3 T TENSOR REMARK 3 T11: 0.2002 T22: 0.1694 REMARK 3 T33: 0.1731 T12: 0.0516 REMARK 3 T13: 0.0036 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 6.0532 L22: 1.9299 REMARK 3 L33: 4.6174 L12: 0.8843 REMARK 3 L13: 2.6999 L23: 0.6787 REMARK 3 S TENSOR REMARK 3 S11: 0.2973 S12: -0.6690 S13: -0.5495 REMARK 3 S21: 0.3997 S22: 0.0707 S23: -0.1418 REMARK 3 S31: 0.4503 S32: -0.0933 S33: -0.3660 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 143:214) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7328 5.3157 -0.3144 REMARK 3 T TENSOR REMARK 3 T11: 0.1530 T22: 0.1643 REMARK 3 T33: 0.1586 T12: 0.0102 REMARK 3 T13: 0.0130 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 2.0965 L22: 1.4129 REMARK 3 L33: 1.2559 L12: 0.0308 REMARK 3 L13: 0.8940 L23: 0.2480 REMARK 3 S TENSOR REMARK 3 S11: -0.0730 S12: -0.2226 S13: -0.0167 REMARK 3 S21: 0.1428 S22: 0.0581 S23: 0.0921 REMARK 3 S31: -0.0429 S32: -0.1713 S33: 0.0193 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 3T4V 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_1000067039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : 20297 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 93.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.852 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 (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2M AMMONIUM SULFATE, REMARK 280 0.1M TRIS-HYDROCHLORIDE PH8.5, 2.2MM AMMONIUM IRON(II) SULFATE, REMARK 280 1MM N-OXALYL-S-(2-NAPTHALENEMETHYL)-L-CYSTEINE, VAPOR DIFFUSION, REMARK 280 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 LYS A 214 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 ARG A 35 CZ NH1 NH2 REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 166 NZ REMARK 470 ASP A 202 OD1 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 OD2 ASP A 133 O3 GOL A 2000 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 A 24 19.51 58.12 REMARK 500 ILE A 201 -105.41 62.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 201 10.32 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 HIS A 131 NE2 REMARK 620 2 ASP A 133 OD1 99.3 REMARK 620 3 HIS A 187 NE2 95.2 91.9 REMARK 620 4 MD3 A 401 O04 109.7 93.0 153.5 REMARK 620 5 MD3 A 401 O03 94.7 165.8 89.6 79.6 REMARK 620 N 1 2 3 4 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 MD3 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2000 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: 3T4H RELATED DB: PDB DBREF 3T4V A 12 216 UNP P05050 ALKB_ECOLI 12 216 SEQADV 3T4V 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 MD3 A 401 23 HET GOL A2000 6 HETNAM FE FE (III) ION HETNAM MD3 N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L- HETNAM 2 MD3 CYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FE FE 3+ FORMUL 3 MD3 C16 H15 N O5 S FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *213(H2 O) HELIX 1 1 ALA A 29 SER A 42 1 14 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 PHE A 209 -1 O TYR A 205 N LEU A 148 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 GLY A 65 -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 SER A 79 N GLY A 68 SHEET 1 C 4 LEU A 128 HIS A 131 0 SHEET 2 C 4 HIS A 187 ILE A 189 -1 O HIS A 187 N HIS A 131 SHEET 3 C 4 ALA A 152 PHE A 156 -1 N GLN A 155 O GLY A 188 SHEET 4 C 4 LYS A 166 LEU A 170 -1 O LEU A 168 N PHE A 154 LINK NE2 HIS A 131 FE FE A 300 1555 1555 2.12 LINK OD1 ASP A 133 FE FE A 300 1555 1555 2.11 LINK NE2 HIS A 187 FE FE A 300 1555 1555 2.05 LINK FE FE A 300 O04 MD3 A 401 1555 1555 2.07 LINK FE FE A 300 O03 MD3 A 401 1555 1555 2.21 SITE 1 AC1 4 HIS A 131 ASP A 133 HIS A 187 MD3 A 401 SITE 1 AC2 19 ASN A 120 TYR A 122 LEU A 128 HIS A 131 SITE 2 AC2 19 ASP A 133 ILE A 143 SER A 145 PHE A 154 SITE 3 AC2 19 TRP A 178 SER A 182 ARG A 183 HIS A 187 SITE 4 AC2 19 ILE A 189 ARG A 204 ASN A 206 THR A 208 SITE 5 AC2 19 ARG A 210 FE A 300 GOL A2000 SITE 1 AC3 6 TRP A 69 HIS A 131 ASP A 133 ARG A 210 SITE 2 AC3 6 MD3 A 401 HOH A 421 CRYST1 37.070 39.234 40.261 76.33 74.56 65.28 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 0.026976 -0.012418 -0.005736 0.00000 SCALE2 0.000000 0.028059 -0.004048 0.00000 SCALE3 0.000000 0.000000 0.026035 0.00000