HEADER OXIDOREDUCTASE 10-FEB-20 6Y0Q TITLE ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB IN COMPLEX WITH FE, AKG TITLE 2 AND METHYLATED DNA UNDER ANAEROBIC ENVIRONMENT USING FT-SSX METHODS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB,DNA OXIDATIVE DEMETHYLASE COMPND 5 ALKB; COMPND 6 EC: 1.14.11.33; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: ALKB, AIDD, B2212, JW2200; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS IRON DEPENDANT DIOXYGENASE, DNA REPAIR, 2-OXOGLUTARATE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.RABE,J.H.BEALE,P.A.LANG,A.S.DIRR,T.M.LEISSING,A.BUTRYN,P.ALLER, AUTHOR 2 J.J.A.G.KAMPS,D.AXFORD,M.A.MCDONOUGH,A.M.ORVILLE,R.OWEN, AUTHOR 3 C.J.SCHOFIELD REVDAT 3 24-JAN-24 6Y0Q 1 REMARK REVDAT 2 30-SEP-20 6Y0Q 1 JRNL REVDAT 1 09-SEP-20 6Y0Q 0 JRNL AUTH P.RABE,J.H.BEALE,A.BUTRYN,P.ALLER,A.DIRR,P.A.LANG, JRNL AUTH 2 D.N.AXFORD,S.B.CARR,T.M.LEISSING,M.A.MCDONOUGH,B.DAVY, JRNL AUTH 3 A.EBRAHIM,J.ORLANS,S.L.S.STORM,A.M.ORVILLE,C.J.SCHOFIELD, JRNL AUTH 4 R.L.OWEN JRNL TITL ANAEROBIC FIXED-TARGET SERIAL CRYSTALLOGRAPHY. JRNL REF IUCRJ V. 7 901 2020 JRNL REFN ESSN 2052-2525 JRNL PMID 32939282 JRNL DOI 10.1107/S2052252520010374 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20267 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) : 0.162 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.849 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 39.6500 - 4.2200 1.00 1307 144 0.1300 0.1500 REMARK 3 2 4.2200 - 3.3500 1.00 1311 141 0.1200 0.1500 REMARK 3 3 3.3500 - 2.9200 1.00 1301 144 0.1400 0.1800 REMARK 3 4 2.9200 - 2.6600 1.00 1311 137 0.1600 0.1900 REMARK 3 5 2.6600 - 2.4700 1.00 1320 143 0.1700 0.1900 REMARK 3 6 2.4700 - 2.3200 1.00 1267 145 0.1700 0.1800 REMARK 3 7 2.3200 - 2.2000 1.00 1333 136 0.1600 0.1800 REMARK 3 8 2.2100 - 2.1100 1.00 1297 150 0.1700 0.2100 REMARK 3 9 2.1100 - 2.0300 1.00 1299 138 0.1900 0.2400 REMARK 3 10 2.0300 - 1.9600 1.00 1303 144 0.1900 0.2300 REMARK 3 11 1.9600 - 1.9000 1.00 1313 148 0.2200 0.2500 REMARK 3 12 1.9000 - 1.8400 1.00 1298 150 0.2400 0.3100 REMARK 3 13 1.8400 - 1.7900 1.00 1309 137 0.2700 0.2900 REMARK 3 14 1.7900 - 1.7500 1.00 1302 139 0.2900 0.2900 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.004 1652 REMARK 3 ANGLE : 0.715 2265 REMARK 3 CHIRALITY : 0.051 240 REMARK 3 PLANARITY : 0.004 296 REMARK 3 DIHEDRAL : 13.509 951 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9208 14.3370 -0.6334 REMARK 3 T TENSOR REMARK 3 T11: 0.2035 T22: 0.1475 REMARK 3 T33: 0.2004 T12: 0.0029 REMARK 3 T13: -0.0071 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 2.5820 L22: 3.9823 REMARK 3 L33: 6.8981 L12: -0.0979 REMARK 3 L13: -1.1439 L23: 0.7051 REMARK 3 S TENSOR REMARK 3 S11: 0.0436 S12: 0.1613 S13: 0.3900 REMARK 3 S21: -0.1913 S22: 0.2017 S23: 0.1340 REMARK 3 S31: -0.6088 S32: -0.5129 S33: -0.0217 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.6049 -6.6593 -6.7642 REMARK 3 T TENSOR REMARK 3 T11: 0.1639 T22: 0.1394 REMARK 3 T33: 0.1476 T12: 0.0084 REMARK 3 T13: -0.0141 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.6065 L22: 2.3101 REMARK 3 L33: 1.2453 L12: 0.1667 REMARK 3 L13: 0.1131 L23: 0.2539 REMARK 3 S TENSOR REMARK 3 S11: -0.0380 S12: 0.0514 S13: -0.1404 REMARK 3 S21: -0.2408 S22: -0.0322 S23: -0.1068 REMARK 3 S31: 0.0862 S32: 0.0295 S33: 0.0325 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4801 -12.2509 6.2184 REMARK 3 T TENSOR REMARK 3 T11: 0.2056 T22: 0.1865 REMARK 3 T33: 0.2448 T12: -0.0222 REMARK 3 T13: -0.0014 T23: 0.0494 REMARK 3 L TENSOR REMARK 3 L11: 2.3608 L22: 1.7462 REMARK 3 L33: 2.0639 L12: 0.0424 REMARK 3 L13: 0.1118 L23: 0.2771 REMARK 3 S TENSOR REMARK 3 S11: -0.1038 S12: -0.2647 S13: -0.7619 REMARK 3 S21: 0.2733 S22: 0.0010 S23: 0.0867 REMARK 3 S31: 0.3306 S32: -0.2710 S33: 0.0364 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8704 -14.0859 -2.8305 REMARK 3 T TENSOR REMARK 3 T11: 0.1347 T22: 0.1562 REMARK 3 T33: 0.2312 T12: 0.0256 REMARK 3 T13: 0.0184 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 1.2686 L22: 5.3575 REMARK 3 L33: 1.7101 L12: 1.6289 REMARK 3 L13: -1.1425 L23: -2.0838 REMARK 3 S TENSOR REMARK 3 S11: -0.0431 S12: 0.1011 S13: -0.0950 REMARK 3 S21: -0.1283 S22: 0.0209 S23: -0.0387 REMARK 3 S31: 0.0486 S32: -0.0307 S33: 0.0558 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4915 7.2123 -3.2381 REMARK 3 T TENSOR REMARK 3 T11: 0.1437 T22: 0.1684 REMARK 3 T33: 0.2336 T12: -0.0260 REMARK 3 T13: 0.0337 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.8726 L22: 7.3676 REMARK 3 L33: 4.0774 L12: -0.9316 REMARK 3 L13: 0.0007 L23: 4.7950 REMARK 3 S TENSOR REMARK 3 S11: 0.0703 S12: 0.0704 S13: 0.2937 REMARK 3 S21: -0.3415 S22: 0.1667 S23: -0.7331 REMARK 3 S31: -0.2905 S32: -0.0288 S33: -0.1648 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 108 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.5103 -0.1200 4.4320 REMARK 3 T TENSOR REMARK 3 T11: 0.1577 T22: 0.1394 REMARK 3 T33: 0.1335 T12: -0.0041 REMARK 3 T13: -0.0080 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.8433 L22: 1.5119 REMARK 3 L33: 1.5323 L12: -0.0321 REMARK 3 L13: 0.3046 L23: 0.1777 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: -0.1261 S13: -0.0499 REMARK 3 S21: 0.1146 S22: 0.0297 S23: -0.0992 REMARK 3 S31: 0.0632 S32: 0.0825 S33: -0.0432 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.0920 7.7937 1.4734 REMARK 3 T TENSOR REMARK 3 T11: 0.1704 T22: 0.1662 REMARK 3 T33: 0.1579 T12: 0.0177 REMARK 3 T13: 0.0004 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.6994 L22: 1.0561 REMARK 3 L33: 1.2726 L12: -0.2161 REMARK 3 L13: 0.4814 L23: 0.2060 REMARK 3 S TENSOR REMARK 3 S11: -0.0622 S12: -0.2146 S13: 0.0106 REMARK 3 S21: 0.0700 S22: 0.0329 S23: 0.0388 REMARK 3 S31: -0.0624 S32: -0.1834 S33: 0.0126 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3955 5.1232 9.7160 REMARK 3 T TENSOR REMARK 3 T11: 0.1459 T22: 0.1881 REMARK 3 T33: 0.1893 T12: 0.0016 REMARK 3 T13: -0.0019 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 3.9583 L22: 1.8435 REMARK 3 L33: 1.3866 L12: 0.8639 REMARK 3 L13: 1.3670 L23: -0.1033 REMARK 3 S TENSOR REMARK 3 S11: 0.0207 S12: -0.5309 S13: 0.1830 REMARK 3 S21: 0.1288 S22: -0.0849 S23: -0.0156 REMARK 3 S31: 0.0748 S32: -0.1329 S33: 0.0113 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 202 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7560 2.7258 -14.3116 REMARK 3 T TENSOR REMARK 3 T11: 0.1817 T22: 0.1538 REMARK 3 T33: 0.1253 T12: -0.0128 REMARK 3 T13: -0.0114 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 2.0429 L22: 0.6858 REMARK 3 L33: 2.0336 L12: 0.3477 REMARK 3 L13: -0.6158 L23: -0.5579 REMARK 3 S TENSOR REMARK 3 S11: -0.0602 S12: 0.1773 S13: 0.0768 REMARK 3 S21: -0.1974 S22: 0.0956 S23: 0.1170 REMARK 3 S31: 0.1224 S32: -0.0864 S33: -0.0308 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 203 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9243 -0.6886 -0.2709 REMARK 3 T TENSOR REMARK 3 T11: 0.1293 T22: 0.1225 REMARK 3 T33: 0.1408 T12: 0.0017 REMARK 3 T13: 0.0002 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 3.7429 L22: 4.1005 REMARK 3 L33: 5.1595 L12: -0.1745 REMARK 3 L13: 1.0660 L23: -0.3213 REMARK 3 S TENSOR REMARK 3 S11: -0.0087 S12: -0.2585 S13: 0.0189 REMARK 3 S21: 0.2128 S22: 0.0178 S23: -0.2273 REMARK 3 S31: -0.0136 S32: 0.1790 S33: 0.0366 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 6Y0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292105255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96863 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 1.8 REMARK 200 DATA SCALING SOFTWARE : DIALS 1.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 39.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 57.57 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4JHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V PEG 3350, 5% V/V GLYCEROL AND REMARK 280 200 MM SODIUM FORMATE, BATCH MODE, TEMPERATURE 298K 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 TOTAL BURIED SURFACE AREA: 540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL 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 1 REMARK 465 LEU A 2 REMARK 465 ASP A 3 REMARK 465 LEU A 4 REMARK 465 PHE A 5 REMARK 465 ALA A 6 REMARK 465 ASP A 7 REMARK 465 ALA A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 TRP A 11 REMARK 465 GLN A 12 REMARK 465 GLU A 13 REMARK 465 PRO A 14 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 LEU A 15 CG CD1 CD2 REMARK 470 ARG A 35 CD NE CZ NH1 NH2 REMARK 470 ARG A 73 CD NE CZ NH1 NH2 REMARK 470 LEU A 77 CD1 REMARK 470 LYS A 87 NZ REMARK 470 GLN A 101 CD OE1 NE2 REMARK 470 LYS A 134 CE NZ REMARK 470 ARG A 140 CZ NH1 NH2 REMARK 470 LYS A 160 CD CE NZ REMARK 470 ARG A 161 NE CZ NH1 NH2 REMARK 470 LYS A 166 CE NZ REMARK 470 LYS A 193 CE NZ REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 LYS A 215 CG CD CE NZ 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 72 137.98 -171.94 REMARK 500 ILE A 201 -74.28 73.23 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 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 NE2 REMARK 620 2 ASP A 133 OD1 91.4 REMARK 620 3 HIS A 187 NE2 88.3 88.7 REMARK 620 4 AKG A 301 O2 96.3 108.8 161.7 REMARK 620 5 AKG A 301 O5 94.9 171.2 85.3 76.7 REMARK 620 6 HOH A 496 O 174.8 91.5 87.5 86.8 81.7 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 AKG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O5W A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JHT RELATED DB: PDB DBREF 6Y0Q A 1 216 UNP P05050 ALKB_ECOLI 1 216 SEQRES 1 A 216 MET LEU ASP LEU PHE ALA ASP ALA GLU PRO TRP GLN GLU SEQRES 2 A 216 PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG ARG PHE ALA SEQRES 3 A 216 PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP ILE ASN ASP SEQRES 4 A 216 VAL ALA SER GLN SER PRO PHE ARG GLN MET VAL THR PRO SEQRES 5 A 216 GLY GLY TYR THR MET SER VAL ALA MET THR ASN CYS GLY SEQRES 6 A 216 HIS LEU GLY TRP THR THR HIS ARG GLN GLY TYR LEU TYR SEQRES 7 A 216 SER PRO ILE ASP PRO GLN THR ASN LYS PRO TRP PRO ALA SEQRES 8 A 216 MET PRO GLN SER PHE HIS ASN LEU CYS GLN ARG ALA ALA SEQRES 9 A 216 THR ALA ALA GLY TYR PRO ASP PHE GLN PRO ASP ALA CYS SEQRES 10 A 216 LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS LEU SER LEU SEQRES 11 A 216 HIS GLN ASP LYS ASP GLU PRO ASP LEU ARG ALA PRO ILE SEQRES 12 A 216 VAL SER VAL SER LEU GLY LEU PRO ALA ILE PHE GLN PHE SEQRES 13 A 216 GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS ARG LEU LEU SEQRES 14 A 216 LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY GLY GLU SER SEQRES 15 A 216 ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU LYS ALA GLY SEQRES 16 A 216 PHE HIS PRO LEU THR ILE ASP CYS ARG TYR ASN LEU THR SEQRES 17 A 216 PHE ARG GLN ALA GLY LYS LYS GLU HET AKG A 301 14 HET FE A 302 1 HET O5W A 303 71 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM FE FE (III) ION HETNAM O5W [(3~{S},5~{R})-5-(6-AZANYL-1-METHYL-PURIN-9-YL)-2- HETNAM 2 O5W (PHOSPHONOOXYMETHYL)OXOLAN-3-YL] [(2~{R},3~{S},5~{R})- HETNAM 3 O5W 5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3- HETNAM 4 O5W OXIDANYL-OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE HETSYN O5W [(1~{R},3~{R})-1-(6-AZANYL-1-METHYL-PURIN-9-YL)-1- HETSYN 2 O5W OXIDANYL-5-PHOSPHONOOXY-PENTAN-3-YL] [(2~{R},3~{S}, HETSYN 3 O5W 5~{R})-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1- HETSYN 4 O5W YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE FORMUL 2 AKG C5 H6 O5 FORMUL 3 FE FE 3+ FORMUL 4 O5W C21 H28 N7 O13 P2 1- FORMUL 5 HOH *136(H2 O) HELIX 1 AA1 ALA A 26 ASN A 28 5 3 HELIX 2 AA2 ALA A 29 SER A 44 1 16 HELIX 3 AA3 PRO A 93 GLY A 108 1 16 HELIX 4 AA4 GLY A 180 PHE A 185 5 6 SHEET 1 AA1 6 ALA A 19 LEU A 22 0 SHEET 2 AA1 6 VAL A 175 TRP A 178 -1 O VAL A 175 N LEU A 22 SHEET 3 AA1 6 ILE A 143 GLY A 149 -1 N SER A 145 O VAL A 176 SHEET 4 AA1 6 ARG A 204 ARG A 210 -1 O TYR A 205 N LEU A 148 SHEET 5 AA1 6 ALA A 116 TYR A 122 -1 N ASN A 120 O ASN A 206 SHEET 6 AA1 6 ALA A 60 GLY A 65 -1 N ALA A 60 O ARG A 121 SHEET 1 AA2 2 GLY A 68 HIS A 72 0 SHEET 2 AA2 2 GLY A 75 SER A 79 -1 O GLY A 75 N HIS A 72 SHEET 1 AA3 4 LEU A 128 HIS A 131 0 SHEET 2 AA3 4 HIS A 187 ILE A 189 -1 O ILE A 189 N LEU A 128 SHEET 3 AA3 4 ALA A 152 PHE A 156 -1 N GLN A 155 O GLY A 188 SHEET 4 AA3 4 LYS A 166 LEU A 170 -1 O LYS A 166 N PHE A 156 LINK NE2 HIS A 131 FE FE A 302 1555 1555 2.17 LINK OD1 ASP A 133 FE FE A 302 1555 1555 2.11 LINK NE2 HIS A 187 FE FE A 302 1555 1555 2.12 LINK O2 AKG A 301 FE FE A 302 1555 1555 2.04 LINK O5 AKG A 301 FE FE A 302 1555 1555 2.40 LINK FE FE A 302 O HOH A 496 1555 1555 2.35 SITE 1 AC1 15 LEU A 118 ASN A 120 TYR A 122 LEU A 128 SITE 2 AC1 15 HIS A 131 ASP A 133 HIS A 187 ILE A 189 SITE 3 AC1 15 ARG A 204 ASN A 206 ARG A 210 FE A 302 SITE 4 AC1 15 O5W A 303 HOH A 427 HOH A 496 SITE 1 AC2 5 HIS A 131 ASP A 133 HIS A 187 AKG A 301 SITE 2 AC2 5 HOH A 496 SITE 1 AC3 19 TYR A 55 THR A 56 MET A 57 HIS A 66 SITE 2 AC3 19 TRP A 69 TYR A 76 LYS A 127 LEU A 128 SITE 3 AC3 19 SER A 129 HIS A 131 ASP A 133 ASP A 135 SITE 4 AC3 19 ARG A 210 AKG A 301 HOH A 402 HOH A 425 SITE 5 AC3 19 HOH A 441 HOH A 477 HOH A 499 CRYST1 36.399 39.078 40.840 78.99 78.04 66.88 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 0.027473 -0.011730 -0.004424 0.00000 SCALE2 0.000000 0.027825 -0.003415 0.00000 SCALE3 0.000000 0.000000 0.025217 0.00000