HEADER METAL BINDING PROTEIN 26-MAY-18 6DJT TITLE STRUCTURE OF TYW1 WITH A LYSINE-PYRUVATE ADDUCT BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYL-L-METHIONINE-DEPENDENT TRNA 4-DEMETHYLWYOSINE COMPND 3 SYNTHASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: MJTYW1,TRNA WYOSINE DERIVATIVES BIOSYNTHESIS PROTEIN TAW1; COMPND 6 EC: 4.1.3.44; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 2190; SOURCE 5 GENE: TAW1, MJ0257; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS S-ADENOSYLMETHIONINE RADICAL ENZYMES, TRNA BIOSYNTHETIC ENZYME, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.A.J.GRELL,C.L.DRENNAN REVDAT 5 29-NOV-23 6DJT 1 REMARK REVDAT 4 11-OCT-23 6DJT 1 REMARK REVDAT 3 27-NOV-19 6DJT 1 REMARK REVDAT 2 20-JUN-18 6DJT 1 JRNL REVDAT 1 13-JUN-18 6DJT 0 JRNL AUTH T.A.J.GRELL,A.P.YOUNG,C.L.DRENNAN,V.BANDARIAN JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF A SCHIFF BASE JRNL TITL 2 IN THE RADICAL-MEDIATED BIOSYNTHESIS OF 4-DEMETHYLWYOSINE BY JRNL TITL 3 TYW1. JRNL REF J. AM. CHEM. SOC. V. 140 6842 2018 JRNL REFN ESSN 1520-5126 JRNL PMID 29792696 JRNL DOI 10.1021/JACS.8B01493 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 47297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2382 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 48.3350 - 4.2159 1.00 2994 166 0.1972 0.2198 REMARK 3 2 4.2159 - 3.3465 1.00 2887 146 0.1417 0.1539 REMARK 3 3 3.3465 - 2.9236 1.00 2830 158 0.1463 0.1685 REMARK 3 4 2.9236 - 2.6563 1.00 2836 146 0.1541 0.1838 REMARK 3 5 2.6563 - 2.4659 1.00 2814 142 0.1574 0.1887 REMARK 3 6 2.4659 - 2.3205 1.00 2792 148 0.1516 0.1856 REMARK 3 7 2.3205 - 2.2043 1.00 2803 150 0.1532 0.2042 REMARK 3 8 2.2043 - 2.1084 1.00 2764 142 0.1531 0.1800 REMARK 3 9 2.1084 - 2.0272 1.00 2800 148 0.1539 0.2072 REMARK 3 10 2.0272 - 1.9572 1.00 2786 146 0.1562 0.1940 REMARK 3 11 1.9572 - 1.8960 0.99 2742 155 0.1764 0.1990 REMARK 3 12 1.8960 - 1.8418 0.98 2723 143 0.2082 0.2280 REMARK 3 13 1.8418 - 1.7934 0.94 2636 132 0.2185 0.2455 REMARK 3 14 1.7934 - 1.7496 0.89 2464 130 0.2293 0.2574 REMARK 3 15 1.7496 - 1.7098 0.81 2212 119 0.2347 0.3051 REMARK 3 16 1.7098 - 1.6734 0.74 2041 120 0.2643 0.2443 REMARK 3 17 1.6734 - 1.6400 0.64 1791 91 0.2886 0.3410 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2778 REMARK 3 ANGLE : 0.841 3770 REMARK 3 CHIRALITY : 0.055 408 REMARK 3 PLANARITY : 0.005 481 REMARK 3 DIHEDRAL : 16.434 1716 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.0734 7.8936 -20.0358 REMARK 3 T TENSOR REMARK 3 T11: 0.3111 T22: 0.2344 REMARK 3 T33: 0.4178 T12: 0.0186 REMARK 3 T13: 0.0774 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 0.0155 L22: 0.1339 REMARK 3 L33: 0.4153 L12: -0.0102 REMARK 3 L13: -0.0321 L23: -0.2092 REMARK 3 S TENSOR REMARK 3 S11: 0.0485 S12: -0.0186 S13: 0.2680 REMARK 3 S21: 0.1831 S22: -0.0705 S23: 0.5938 REMARK 3 S31: -0.5910 S32: 0.0073 S33: -0.0213 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8269 8.5785 -19.8008 REMARK 3 T TENSOR REMARK 3 T11: 0.3182 T22: 0.2571 REMARK 3 T33: 0.2246 T12: -0.0305 REMARK 3 T13: -0.0235 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 0.0648 L22: 0.0353 REMARK 3 L33: 0.0386 L12: -0.0368 REMARK 3 L13: 0.0640 L23: -0.0274 REMARK 3 S TENSOR REMARK 3 S11: -0.1112 S12: -0.1334 S13: 0.0294 REMARK 3 S21: 0.1238 S22: -0.0735 S23: -0.0519 REMARK 3 S31: -0.3302 S32: 0.1601 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.7070 0.4730 -20.0072 REMARK 3 T TENSOR REMARK 3 T11: 0.2467 T22: 0.2437 REMARK 3 T33: 0.2398 T12: -0.0123 REMARK 3 T13: 0.0309 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.0585 L22: 0.1072 REMARK 3 L33: -0.0128 L12: -0.0887 REMARK 3 L13: 0.0161 L23: -0.0330 REMARK 3 S TENSOR REMARK 3 S11: 0.1122 S12: -0.1200 S13: 0.1602 REMARK 3 S21: 0.1680 S22: -0.0639 S23: 0.2341 REMARK 3 S31: -0.2130 S32: 0.0778 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0868 -3.1489 -17.0134 REMARK 3 T TENSOR REMARK 3 T11: 0.3958 T22: 0.3374 REMARK 3 T33: 0.4855 T12: -0.0473 REMARK 3 T13: 0.0006 T23: -0.0699 REMARK 3 L TENSOR REMARK 3 L11: 0.0711 L22: 0.1341 REMARK 3 L33: 0.0932 L12: -0.0106 REMARK 3 L13: -0.0020 L23: -0.1139 REMARK 3 S TENSOR REMARK 3 S11: -0.1458 S12: 0.0135 S13: 0.1839 REMARK 3 S21: 0.2852 S22: 0.1291 S23: 0.2357 REMARK 3 S31: -0.3279 S32: 0.0490 S33: -0.0010 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2281 11.0831 -30.3504 REMARK 3 T TENSOR REMARK 3 T11: 0.2866 T22: 0.2125 REMARK 3 T33: 0.2838 T12: 0.0242 REMARK 3 T13: -0.0004 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.0859 L22: 0.1416 REMARK 3 L33: 0.0838 L12: -0.0782 REMARK 3 L13: -0.0629 L23: -0.0664 REMARK 3 S TENSOR REMARK 3 S11: -0.0228 S12: 0.1204 S13: 0.1208 REMARK 3 S21: -0.2666 S22: 0.0970 S23: -0.0054 REMARK 3 S31: -0.1553 S32: -0.0404 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 154 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3730 0.3139 -28.3962 REMARK 3 T TENSOR REMARK 3 T11: 0.2648 T22: 0.2017 REMARK 3 T33: 0.1970 T12: -0.0077 REMARK 3 T13: 0.0057 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.3026 L22: 0.1315 REMARK 3 L33: 0.0628 L12: -0.0606 REMARK 3 L13: 0.0592 L23: -0.1394 REMARK 3 S TENSOR REMARK 3 S11: -0.0396 S12: 0.0520 S13: 0.0741 REMARK 3 S21: -0.2747 S22: -0.0107 S23: 0.1442 REMARK 3 S31: 0.0701 S32: 0.0482 S33: -0.0002 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 155 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1852 -13.0746 -12.3527 REMARK 3 T TENSOR REMARK 3 T11: 0.2679 T22: 0.2000 REMARK 3 T33: 0.2072 T12: 0.0103 REMARK 3 T13: 0.0376 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.6765 L22: 0.4854 REMARK 3 L33: 0.3296 L12: 0.1601 REMARK 3 L13: 0.3295 L23: 0.0752 REMARK 3 S TENSOR REMARK 3 S11: -0.0125 S12: -0.0619 S13: -0.0625 REMARK 3 S21: -0.0020 S22: -0.0201 S23: 0.0339 REMARK 3 S31: 0.3438 S32: 0.0954 S33: 0.0001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 311 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1240 -5.5103 -6.3137 REMARK 3 T TENSOR REMARK 3 T11: 0.2218 T22: 0.2286 REMARK 3 T33: 0.1865 T12: 0.0393 REMARK 3 T13: -0.0041 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.9069 L22: 0.4828 REMARK 3 L33: 0.8886 L12: 0.6354 REMARK 3 L13: 0.3251 L23: -0.0710 REMARK 3 S TENSOR REMARK 3 S11: -0.0018 S12: -0.0782 S13: 0.0495 REMARK 3 S21: 0.1414 S22: -0.0755 S23: -0.0211 REMARK 3 S31: -0.0264 S32: 0.1616 S33: -0.0001 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 6DJT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47373 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.68900 REMARK 200 FOR SHELL : 2.200 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: 2Z2U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM POTASSIUM PHOSPHATE MONOBASIC REMARK 280 /SODIUM PHOSPHATE DIBASIC PH 6.2, 10% (W/V) PEG 3000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 29.13000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.22800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.05450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.22800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.13000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.05450 REMARK 290 SMTRY3 4 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 LEU A 73 REMARK 465 PRO A 74 REMARK 465 ARG A 75 REMARK 465 ASP A 76 REMARK 465 ILE A 77 REMARK 465 GLY A 78 REMARK 465 ILE A 79 REMARK 465 ASP A 80 REMARK 465 ILE A 81 REMARK 465 GLY A 256 REMARK 465 TYR A 257 REMARK 465 SER A 258 REMARK 465 GLN A 259 REMARK 465 LYS A 260 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 5 OE1 OE2 REMARK 470 LYS A 8 CD CE NZ REMARK 470 LYS A 31 CE NZ REMARK 470 TRP A 70 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 70 CZ3 CH2 REMARK 470 ARG A 71 CZ NH1 NH2 REMARK 470 VAL A 72 CG1 CG2 REMARK 470 SER A 82 OG REMARK 470 GLN A 83 CG CD OE1 NE2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 GLU A 237 CD OE1 OE2 REMARK 470 VAL A 255 CG1 CG2 REMARK 470 ARG A 261 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 263 CD CE NZ REMARK 470 LYS A 264 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 ASN A 65 64.29 -150.85 REMARK 500 SER A 134 14.30 -161.78 REMARK 500 ASN A 229 22.43 -142.48 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 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 26 SG REMARK 620 2 SF4 A 401 S1 113.9 REMARK 620 3 SF4 A 401 S2 111.7 104.2 REMARK 620 4 SF4 A 401 S3 117.7 104.1 103.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 SF4 A 401 S2 109.8 REMARK 620 3 SF4 A 401 S3 108.8 104.8 REMARK 620 4 SF4 A 401 S4 126.4 102.6 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KPI A 41 NZ REMARK 620 2 SF4 A 401 S1 136.8 REMARK 620 3 SF4 A 401 S3 115.1 104.3 REMARK 620 4 SF4 A 401 S4 95.0 99.1 94.4 REMARK 620 5 KPI A 41 NZ 18.1 144.9 98.9 105.1 REMARK 620 6 KPI A 41 O2 65.9 89.7 102.2 158.7 59.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 52 SG REMARK 620 2 SF4 A 401 S1 109.7 REMARK 620 3 SF4 A 401 S2 113.0 104.8 REMARK 620 4 SF4 A 401 S4 118.3 105.1 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FS0 A 412 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 FS0 A 412 S5 106.4 REMARK 620 3 FS0 A 412 S1 110.6 108.4 REMARK 620 4 FS0 A 412 S2 119.7 106.4 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FS0 A 412 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 FS0 A 412 S1 108.1 REMARK 620 3 FS0 A 412 S2 115.0 105.2 REMARK 620 4 CYS A 69 SG 106.0 116.3 106.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FS0 A 412 DBREF 6DJT A 1 311 UNP Q57705 TYW1_METJA 1 311 SEQADV 6DJT MET A -19 UNP Q57705 EXPRESSION TAG SEQADV 6DJT GLY A -18 UNP Q57705 EXPRESSION TAG SEQADV 6DJT SER A -17 UNP Q57705 EXPRESSION TAG SEQADV 6DJT SER A -16 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A -15 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A -14 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A -13 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A -12 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A -11 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A -10 UNP Q57705 EXPRESSION TAG SEQADV 6DJT SER A -9 UNP Q57705 EXPRESSION TAG SEQADV 6DJT SER A -8 UNP Q57705 EXPRESSION TAG SEQADV 6DJT GLY A -7 UNP Q57705 EXPRESSION TAG SEQADV 6DJT LEU A -6 UNP Q57705 EXPRESSION TAG SEQADV 6DJT VAL A -5 UNP Q57705 EXPRESSION TAG SEQADV 6DJT PRO A -4 UNP Q57705 EXPRESSION TAG SEQADV 6DJT ARG A -3 UNP Q57705 EXPRESSION TAG SEQADV 6DJT GLY A -2 UNP Q57705 EXPRESSION TAG SEQADV 6DJT SER A -1 UNP Q57705 EXPRESSION TAG SEQADV 6DJT HIS A 0 UNP Q57705 EXPRESSION TAG SEQRES 1 A 331 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 331 LEU VAL PRO ARG GLY SER HIS MET ILE PRO GLU GLU ILE SEQRES 3 A 331 TYR LYS ILE LEU ARG LYS GLN ARG TYR GLN ILE ASP GLY SEQRES 4 A 331 HIS THR ALA VAL LYS LEU CYS GLY TRP VAL ARG LYS LYS SEQRES 5 A 331 MET LEU GLU ASP LYS ASN CYS TYR KPI SER LYS PHE TYR SEQRES 6 A 331 GLY ILE GLU THR HIS ARG CYS ILE GLN CYS THR PRO SER SEQRES 7 A 331 VAL ILE TRP CYS GLN GLN ASN CYS ILE PHE CYS TRP ARG SEQRES 8 A 331 VAL LEU PRO ARG ASP ILE GLY ILE ASP ILE SER GLN ILE SEQRES 9 A 331 LYS GLU PRO LYS TRP GLU GLU PRO GLU VAL VAL TYR GLU SEQRES 10 A 331 LYS ILE LEU ALA MET HIS LYS ARG ILE ILE MET GLY TYR SEQRES 11 A 331 ALA GLY VAL LEU ASP ARG VAL GLY GLU LYS LYS PHE LYS SEQRES 12 A 331 GLU ALA LEU GLU PRO LYS HIS VAL ALA ILE SER LEU SER SEQRES 13 A 331 GLY GLU PRO THR LEU TYR PRO TYR LEU ASP GLU LEU ILE SEQRES 14 A 331 LYS ILE PHE HIS LYS ASN GLY PHE THR THR PHE VAL VAL SEQRES 15 A 331 SER ASN GLY ILE LEU THR ASP VAL ILE GLU LYS ILE GLU SEQRES 16 A 331 PRO THR GLN LEU TYR ILE SER LEU ASP ALA TYR ASP LEU SEQRES 17 A 331 ASP SER TYR ARG ARG ILE CYS GLY GLY LYS LYS GLU TYR SEQRES 18 A 331 TRP GLU SER ILE LEU ASN THR LEU ASP ILE LEU LYS GLU SEQRES 19 A 331 LYS LYS ARG THR CYS ILE ARG THR THR LEU ILE ARG GLY SEQRES 20 A 331 TYR ASN ASP ASP ILE LEU LYS PHE VAL GLU LEU TYR GLU SEQRES 21 A 331 ARG ALA ASP VAL HIS PHE ILE GLU LEU LYS SER TYR MET SEQRES 22 A 331 HIS VAL GLY TYR SER GLN LYS ARG LEU LYS LYS GLU ASP SEQRES 23 A 331 MET LEU GLN HIS ASP GLU ILE LEU LYS LEU ALA LYS MET SEQRES 24 A 331 LEU ASP GLU ASN SER SER TYR LYS LEU ILE ASP ASP SER SEQRES 25 A 331 GLU ASP SER ARG VAL ALA LEU LEU GLN ASN GLU ASN ARG SEQRES 26 A 331 LYS ILE ASN PRO LYS LEU MODRES 6DJT KPI A 41 LYS MODIFIED RESIDUE HET KPI A 41 28 HET SF4 A 401 8 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HET GOL A 408 6 HET GOL A 409 6 HET PEG A 410 7 HET PEG A 411 7 HET FS0 A 412 5 HETNAM KPI (2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE) HETNAM 2 KPI AMINO]HEXANOIC ACID HETNAM SF4 IRON/SULFUR CLUSTER HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM FS0 FE2/S3 CLUSTER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 KPI C9 H16 N2 O4 FORMUL 2 SF4 FE4 S4 FORMUL 3 GOL 8(C3 H8 O3) FORMUL 11 PEG 2(C4 H10 O3) FORMUL 13 FS0 FE2 H S3 FORMUL 14 HOH *191(H2 O) HELIX 1 AA1 PRO A 3 GLN A 13 1 11 HELIX 2 AA2 CYS A 26 ASP A 36 1 11 HELIX 3 AA3 CYS A 39 GLY A 46 1 8 HELIX 4 AA4 GLU A 48 HIS A 50 5 3 HELIX 5 AA5 GLU A 91 GLY A 109 1 19 HELIX 6 AA6 TYR A 110 GLY A 112 5 3 HELIX 7 AA7 VAL A 113 GLY A 118 1 6 HELIX 8 AA8 GLY A 118 LEU A 126 1 9 HELIX 9 AA9 GLU A 138 TYR A 142 5 5 HELIX 10 AB1 TYR A 144 ASN A 155 1 12 HELIX 11 AB2 LEU A 167 ILE A 174 1 8 HELIX 12 AB3 ASP A 187 GLY A 196 1 10 HELIX 13 AB4 LYS A 198 LEU A 212 1 15 HELIX 14 AB5 LYS A 213 LYS A 215 5 3 HELIX 15 AB6 ASP A 231 LYS A 234 5 4 HELIX 16 AB7 PHE A 235 ASP A 243 1 9 HELIX 17 AB8 LYS A 263 MET A 267 5 5 HELIX 18 AB9 GLN A 269 ASN A 283 1 15 HELIX 19 AC1 GLU A 293 SER A 295 5 3 SHEET 1 AA110 GLN A 16 ASP A 18 0 SHEET 2 AA110 THR A 21 VAL A 23 -1 O VAL A 23 N GLN A 16 SHEET 3 AA110 CYS A 52 THR A 56 -1 O THR A 56 N ALA A 22 SHEET 4 AA110 HIS A 130 ILE A 133 1 O ALA A 132 N ILE A 53 SHEET 5 AA110 THR A 158 SER A 163 1 O PHE A 160 N ILE A 133 SHEET 6 AA110 GLN A 178 SER A 182 1 O TYR A 180 N VAL A 161 SHEET 7 AA110 THR A 218 LEU A 224 1 O CYS A 219 N LEU A 179 SHEET 8 AA110 PHE A 246 SER A 251 1 O LYS A 250 N LEU A 224 SHEET 9 AA110 VAL A 297 ASN A 302 -1 O LEU A 300 N ILE A 247 SHEET 10 AA110 TYR A 286 SER A 292 -1 N ILE A 289 O LEU A 299 LINK C TYR A 40 N AKPI A 41 1555 1555 1.33 LINK C TYR A 40 N BKPI A 41 1555 1555 1.33 LINK C AKPI A 41 N SER A 42 1555 1555 1.33 LINK C BKPI A 41 N SER A 42 1555 1555 1.33 LINK SG CYS A 26 FE4 SF4 A 401 1555 1555 2.29 LINK SG CYS A 39 FE1 SF4 A 401 1555 1555 2.35 LINK NZ AKPI A 41 FE2 SF4 A 401 1555 1555 2.37 LINK NZ BKPI A 41 FE2 SF4 A 401 1555 1555 2.54 LINK O2 AKPI A 41 FE2 SF4 A 401 1555 1555 2.45 LINK SG ACYS A 52 FE3 SF4 A 401 1555 1555 2.27 LINK SG CYS A 62 FE2 FS0 A 412 1555 1555 2.32 LINK SG CYS A 66 FE1 FS0 A 412 1555 1555 2.35 LINK SG CYS A 69 FE1 FS0 A 412 1555 1555 2.34 SITE 1 AC1 4 CYS A 26 CYS A 39 KPI A 41 CYS A 52 SITE 1 AC2 7 LEU A 100 LEU A 126 PRO A 128 MET A 279 SITE 2 AC2 7 HOH A 515 HOH A 553 HOH A 558 SITE 1 AC3 9 GLU A 127 LYS A 129 ASN A 155 ARG A 226 SITE 2 AC3 9 ASP A 230 GLU A 272 LYS A 275 HOH A 554 SITE 3 AC3 9 HOH A 582 SITE 1 AC4 4 LYS A 43 SER A 292 GLU A 293 ASP A 294 SITE 1 AC5 5 SER A 134 GLY A 137 PRO A 139 VAL A 162 SITE 2 AC5 5 HOH A 564 SITE 1 AC6 8 GLN A 63 ALA A 111 GLY A 112 VAL A 113 SITE 2 AC6 8 LEU A 114 ASP A 115 TYR A 201 HOH A 608 SITE 1 AC7 8 TYR A 186 GLY A 227 TYR A 228 ASN A 229 SITE 2 AC7 8 ASP A 230 ASP A 231 LYS A 234 HOH A 537 SITE 1 AC8 6 LYS A 120 TYR A 186 ASP A 187 ASP A 189 SITE 2 AC8 6 ARG A 193 LYS A 234 SITE 1 AC9 4 LYS A 264 GLU A 265 MET A 267 ARG A 296 SITE 1 AD1 1 GLN A 301 SITE 1 AD2 7 ARG A 11 ARG A 14 GLU A 172 GLU A 175 SITE 2 AD2 7 GLU A 214 LYS A 215 HOH A 505 SITE 1 AD3 7 CYS A 62 GLN A 64 ASN A 65 CYS A 66 SITE 2 AD3 7 CYS A 69 GLY A 137 HOH A 662 CRYST1 58.260 80.109 86.456 90.00 90.00 90.00 P 21 21 21 4 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 0.017164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011567 0.00000