HEADER TRANSFERASE 07-AUG-19 6Q2E TITLE CRYSTAL STRUCTURE OF METHANOBREVIBACTER SMITHII DPH2 BOUND TO 5'- TITLE 2 METHYLTHIOADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-(3-AMINO-3-CARBOXYPROPYL)HISTIDINE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPH2; COMPND 5 EC: 2.5.1.108; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOBREVIBACTER SMITHII; SOURCE 3 ORGANISM_TAXID: 2173; SOURCE 4 GENE: MSM_1358; 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: PET28A KEYWDS RADICAL, S-ADENOSYLMETHIONINE, ENZYME, IRON SULFUR CLUSTER, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.FENWICK,M.DONG,H.LIN,S.E.EALICK REVDAT 5 11-OCT-23 6Q2E 1 REMARK REVDAT 4 04-DEC-19 6Q2E 1 REMARK REVDAT 3 13-NOV-19 6Q2E 1 JRNL REVDAT 2 06-NOV-19 6Q2E 1 JRNL REVDAT 1 16-OCT-19 6Q2E 0 JRNL AUTH M.K.FENWICK,M.DONG,H.LIN,S.E.EALICK JRNL TITL THE CRYSTAL STRUCTURE OF DPH2 IN COMPLEX WITH ELONGATION JRNL TITL 2 FACTOR 2 REVEALS THE STRUCTURAL BASIS FOR THE FIRST STEP OF JRNL TITL 3 DIPHTHAMIDE BIOSYNTHESIS. JRNL REF BIOCHEMISTRY V. 58 4343 2019 JRNL REFN ISSN 0006-2960 JRNL PMID 31566354 JRNL DOI 10.1021/ACS.BIOCHEM.9B00718 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3211 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 64546 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 3157 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 68.9000 - 5.0273 0.96 2834 152 0.1711 0.1946 REMARK 3 2 5.0273 - 3.9904 0.99 2801 136 0.1367 0.1596 REMARK 3 3 3.9904 - 3.4860 0.99 2762 135 0.1405 0.1723 REMARK 3 4 3.4860 - 3.1673 0.99 2761 137 0.1739 0.2147 REMARK 3 5 3.1673 - 2.9403 0.95 2612 141 0.1842 0.2349 REMARK 3 6 2.9403 - 2.7669 0.98 2702 137 0.1989 0.2622 REMARK 3 7 2.7669 - 2.6283 0.99 2691 142 0.2044 0.2808 REMARK 3 8 2.6283 - 2.5139 0.98 2716 123 0.2044 0.2525 REMARK 3 9 2.5139 - 2.4171 0.98 2714 134 0.2055 0.2612 REMARK 3 10 2.4171 - 2.3337 0.99 2658 157 0.2048 0.2196 REMARK 3 11 2.3337 - 2.2608 0.98 2689 131 0.2048 0.2349 REMARK 3 12 2.2608 - 2.1961 0.98 2715 111 0.2097 0.2461 REMARK 3 13 2.1961 - 2.1383 0.98 2613 156 0.2014 0.2822 REMARK 3 14 2.1383 - 2.0861 0.98 2705 138 0.2058 0.2839 REMARK 3 15 2.0861 - 2.0387 0.95 2606 123 0.2081 0.2587 REMARK 3 16 2.0387 - 1.9953 0.97 2638 134 0.2090 0.2308 REMARK 3 17 1.9953 - 1.9554 0.98 2639 157 0.2186 0.2504 REMARK 3 18 1.9554 - 1.9185 0.98 2638 144 0.2264 0.2767 REMARK 3 19 1.9185 - 1.8842 0.97 2649 149 0.2299 0.2756 REMARK 3 20 1.8842 - 1.8523 0.98 2621 138 0.2391 0.2718 REMARK 3 21 1.8523 - 1.8224 0.96 2636 122 0.2484 0.3470 REMARK 3 22 1.8224 - 1.7944 0.97 2604 122 0.2645 0.3038 REMARK 3 23 1.7944 - 1.7680 0.89 2385 138 0.2852 0.3062 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.45 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0004 41.7543 -7.7681 REMARK 3 T TENSOR REMARK 3 T11: 0.2626 T22: 0.1597 REMARK 3 T33: 0.1926 T12: -0.0147 REMARK 3 T13: 0.0251 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 6.0293 L22: 0.7651 REMARK 3 L33: 2.1727 L12: -0.6690 REMARK 3 L13: 0.5541 L23: -0.1648 REMARK 3 S TENSOR REMARK 3 S11: -0.0483 S12: 0.0867 S13: 0.1224 REMARK 3 S21: -0.1083 S22: 0.0243 S23: 0.0217 REMARK 3 S31: -0.1140 S32: -0.0894 S33: 0.0291 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 114 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7328 45.1794 -8.3781 REMARK 3 T TENSOR REMARK 3 T11: 0.2498 T22: 0.2967 REMARK 3 T33: 0.2556 T12: 0.0620 REMARK 3 T13: -0.0110 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 5.1132 L22: 3.1938 REMARK 3 L33: 9.1190 L12: 0.6880 REMARK 3 L13: 1.7407 L23: 0.6499 REMARK 3 S TENSOR REMARK 3 S11: -0.1187 S12: 0.0865 S13: 0.3070 REMARK 3 S21: -0.0723 S22: -0.0603 S23: 0.1713 REMARK 3 S31: 0.0323 S32: -0.4095 S33: 0.1403 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 209 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0608 43.2616 18.5607 REMARK 3 T TENSOR REMARK 3 T11: 0.2321 T22: 0.1753 REMARK 3 T33: 0.2191 T12: 0.0203 REMARK 3 T13: 0.0564 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 4.6861 L22: 1.6047 REMARK 3 L33: 2.8492 L12: -0.0814 REMARK 3 L13: -0.2456 L23: -0.0662 REMARK 3 S TENSOR REMARK 3 S11: -0.1521 S12: -0.1209 S13: -0.1605 REMARK 3 S21: 0.0672 S22: 0.0679 S23: 0.2087 REMARK 3 S31: 0.1934 S32: -0.2504 S33: 0.0572 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5171 45.2127 31.9041 REMARK 3 T TENSOR REMARK 3 T11: 0.2651 T22: 0.4017 REMARK 3 T33: 0.2376 T12: 0.0379 REMARK 3 T13: -0.0193 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 5.4961 L22: 6.4314 REMARK 3 L33: 6.0422 L12: -1.1130 REMARK 3 L13: 0.7231 L23: 0.2538 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: -0.6885 S13: 0.1348 REMARK 3 S21: 0.4916 S22: 0.0419 S23: -0.4335 REMARK 3 S31: 0.0626 S32: 0.2718 S33: -0.0275 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 63 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1383 34.7745 34.7088 REMARK 3 T TENSOR REMARK 3 T11: 0.2501 T22: 0.2823 REMARK 3 T33: 0.2929 T12: -0.0375 REMARK 3 T13: 0.0020 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 4.0397 L22: 4.6060 REMARK 3 L33: 1.1918 L12: -3.1088 REMARK 3 L13: 0.9793 L23: -1.0986 REMARK 3 S TENSOR REMARK 3 S11: 0.0229 S12: 0.0937 S13: 0.2947 REMARK 3 S21: 0.2092 S22: -0.1598 S23: -0.1919 REMARK 3 S31: -0.0019 S32: 0.0835 S33: 0.1449 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 141 THROUGH 207 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.6069 25.7003 30.8166 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.2363 REMARK 3 T33: 0.3268 T12: -0.0023 REMARK 3 T13: -0.0119 T23: -0.0256 REMARK 3 L TENSOR REMARK 3 L11: 2.1444 L22: 1.8710 REMARK 3 L33: 7.8821 L12: -0.8443 REMARK 3 L13: -0.7354 L23: -1.1558 REMARK 3 S TENSOR REMARK 3 S11: 0.0628 S12: 0.1592 S13: 0.0759 REMARK 3 S21: 0.1097 S22: -0.1912 S23: -0.1039 REMARK 3 S31: 0.0950 S32: 0.1840 S33: 0.0791 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 208 THROUGH 330 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4014 26.2194 7.4760 REMARK 3 T TENSOR REMARK 3 T11: 0.2253 T22: 0.1914 REMARK 3 T33: 0.2413 T12: 0.0281 REMARK 3 T13: 0.0077 T23: -0.0483 REMARK 3 L TENSOR REMARK 3 L11: 2.3993 L22: 2.4829 REMARK 3 L33: 3.7692 L12: -0.9030 REMARK 3 L13: 1.7347 L23: -0.4813 REMARK 3 S TENSOR REMARK 3 S11: 0.1531 S12: 0.0309 S13: -0.1768 REMARK 3 S21: 0.0743 S22: 0.0509 S23: -0.0763 REMARK 3 S31: 0.4085 S32: 0.1205 S33: -0.1855 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 6Q2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-18 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.768 REMARK 200 RESOLUTION RANGE LOW (A) : 131.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: CANDIDATUS METHANOPEREDENS NITROREDUCENS DPH2 REMARK 200 BOUND TO S-ADENOSYLHOMOCYSTEINE (PDB ENTRY 6BXO) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BISTRISPROPANE, PH 6.5, 16-17 % REMARK 280 (W/V) PEG2000 MONOMETHYL ETHER, 6 MM 5'-METHYLTHIOADENOSINE AND REMARK 280 14 MM 2-AMINOBUTYRATE. AFTER DROPS WERE FORMED BY COMBINING THE REMARK 280 SAMPLE AND RESERVOIR SOLUTIONS, 300 MM NACL WAS ADDED TO THE REMARK 280 RESERVOIRS PRIOR TO SEALING, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 31.54100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.48600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.48600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.54100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.51000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 330 REMARK 465 GLU A 331 REMARK 465 ARG A 332 REMARK 465 TYR A 333 REMARK 465 LYS A 334 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLU B 331 REMARK 465 ARG B 332 REMARK 465 TYR B 333 REMARK 465 LYS B 334 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 LYS A 17 CG CD CE NZ REMARK 470 LYS A 18 CG CD CE NZ REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 SER A 150 OG REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 LYS A 155 CG CD CE NZ REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 LYS A 246 CG CD CE NZ REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 LYS B 14 CG CD CE NZ REMARK 470 LYS B 17 CG CD CE NZ REMARK 470 LYS B 18 CG CD CE NZ REMARK 470 ARG B 21 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 LYS B 37 CG CD CE NZ REMARK 470 LYS B 69 CG CD CE NZ REMARK 470 LYS B 86 CG CD CE NZ REMARK 470 GLU B 88 CG CD OE1 OE2 REMARK 470 GLU B 107 CG CD OE1 OE2 REMARK 470 LYS B 118 CG CD CE NZ REMARK 470 LYS B 154 CG CD CE NZ REMARK 470 ASP B 170 CG OD1 OD2 REMARK 470 LYS B 253 CG CD CE NZ REMARK 470 LYS B 259 CG CD CE NZ REMARK 470 GLN B 298 CG CD OE1 NE2 REMARK 470 LYS B 301 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 PRO A 200 2.36 -66.63 REMARK 500 ASP A 268 -78.45 -77.71 REMARK 500 ALA A 288 -147.98 -89.75 REMARK 500 GLU B 88 -71.08 -62.62 REMARK 500 ASP B 268 -82.10 -77.68 REMARK 500 SER B 287 41.66 -103.76 REMARK 500 ALA B 288 -143.10 -127.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 760 DISTANCE = 6.95 ANGSTROMS 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 402 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 SF4 A 402 S2 111.6 REMARK 620 3 SF4 A 402 S3 115.9 104.7 REMARK 620 4 SF4 A 402 S4 115.0 102.8 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 402 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 161 SG REMARK 620 2 SF4 A 402 S1 113.0 REMARK 620 3 SF4 A 402 S3 108.5 107.4 REMARK 620 4 SF4 A 402 S4 117.7 102.6 106.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 402 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 289 SG REMARK 620 2 SF4 A 402 S1 113.8 REMARK 620 3 SF4 A 402 S2 114.5 102.3 REMARK 620 4 SF4 A 402 S4 112.9 105.0 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 402 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 61 SG REMARK 620 2 SF4 B 402 S2 109.9 REMARK 620 3 SF4 B 402 S3 115.2 104.1 REMARK 620 4 SF4 B 402 S4 119.9 103.9 102.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 402 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 161 SG REMARK 620 2 SF4 B 402 S1 115.0 REMARK 620 3 SF4 B 402 S3 117.1 107.5 REMARK 620 4 SF4 B 402 S4 109.9 101.3 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 402 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 289 SG REMARK 620 2 SF4 B 402 S1 115.1 REMARK 620 3 SF4 B 402 S2 110.9 105.0 REMARK 620 4 SF4 B 402 S4 113.1 102.6 109.7 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 MTA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MTA B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 B 402 DBREF 6Q2E A 1 334 UNP A5UMY5 A5UMY5_METS3 1 334 DBREF 6Q2E B 1 334 UNP A5UMY5 A5UMY5_METS3 1 334 SEQADV 6Q2E GLY A -2 UNP A5UMY5 EXPRESSION TAG SEQADV 6Q2E SER A -1 UNP A5UMY5 EXPRESSION TAG SEQADV 6Q2E HIS A 0 UNP A5UMY5 EXPRESSION TAG SEQADV 6Q2E GLY B -2 UNP A5UMY5 EXPRESSION TAG SEQADV 6Q2E SER B -1 UNP A5UMY5 EXPRESSION TAG SEQADV 6Q2E HIS B 0 UNP A5UMY5 EXPRESSION TAG SEQRES 1 A 337 GLY SER HIS MET SER MET TYR ASN MET ASP LEU ASP LYS SEQRES 2 A 337 VAL ILE ARG LYS ILE ASN LYS LYS GLY ALA ARG THR VAL SEQRES 3 A 337 GLY LEU GLN PHE PRO GLU GLY LEU LYS MET GLN ALA VAL SEQRES 4 A 337 LYS ILE ALA LYS ALA ILE GLU SER GLN THR PRO ALA THR SEQRES 5 A 337 VAL ILE ILE SER GLY ASP PRO CYS PHE GLY ALA CYS ASP SEQRES 6 A 337 VAL SER ASP TYR LYS MET LYS GLY SER VAL ASP LEU ILE SEQRES 7 A 337 VAL HIS TYR GLY HIS THR PRO LEU PRO LEU LYS TYR GLU SEQRES 8 A 337 VAL PRO THR LEU PHE ILE GLU ALA PHE SER ASN ILE ASP SEQRES 9 A 337 VAL LYS LYS ASP LEU GLU LYS CYS LEU GLU LYS LEU GLU SEQRES 10 A 337 ASP TYR SER LYS ILE ALA LEU VAL THR THR THR GLN HIS SEQRES 11 A 337 LEU HIS LEU LEU ASN GLU ILE LYS ASP TYR LEU GLU ASP SEQRES 12 A 337 ASN GLY LYS GLU VAL VAL LEU GLY SER SER LYS ASN THR SEQRES 13 A 337 LYS LYS GLY GLN VAL LEU GLY CYS ASN PHE SER SER ILE SEQRES 14 A 337 LYS ASN LEU ASP ALA GLU VAL TYR LEU PHE ILE GLY SER SEQRES 15 A 337 GLY ASN PHE HIS PRO LEU GLY ILE TYR LEU PHE THR LYS SEQRES 16 A 337 SER PRO VAL LEU ALA LEU ASP PRO TYR ASN SER GLU ILE SEQRES 17 A 337 ARG ASP ILE SER ALA PHE ALA ASP ARG ILE LEU ARG ILE SEQRES 18 A 337 ARG PHE ALA ARG ILE THR LYS ALA ARG GLU ALA GLU LYS SEQRES 19 A 337 TRP GLY ILE ILE VAL SER SER LYS GLU GLY GLN TYR ARG SEQRES 20 A 337 MET LYS LEU ALA LYS GLU ILE LYS LYS ILE LEU GLU ASP SEQRES 21 A 337 ASN LYS MET GLU ALA TYR ILE ILE MET ALA ASP ASN ILE SEQRES 22 A 337 ASN PRO ASP ILE LEU LEU PRO TYR MET GLU LEU ASP ALA SEQRES 23 A 337 PHE VAL VAL SER ALA CYS PRO ARG ILE ALA ILE ASP ASP SEQRES 24 A 337 SER GLN MET TYR LYS LYS PRO LEU LEU THR PRO GLN GLU SEQRES 25 A 337 LEU GLU ILE VAL LEU ASN LYS ARG GLN TRP GLU ASN TYR SEQRES 26 A 337 GLN LEU ASP GLU ILE LEU PHE HIS GLU ARG TYR LYS SEQRES 1 B 337 GLY SER HIS MET SER MET TYR ASN MET ASP LEU ASP LYS SEQRES 2 B 337 VAL ILE ARG LYS ILE ASN LYS LYS GLY ALA ARG THR VAL SEQRES 3 B 337 GLY LEU GLN PHE PRO GLU GLY LEU LYS MET GLN ALA VAL SEQRES 4 B 337 LYS ILE ALA LYS ALA ILE GLU SER GLN THR PRO ALA THR SEQRES 5 B 337 VAL ILE ILE SER GLY ASP PRO CYS PHE GLY ALA CYS ASP SEQRES 6 B 337 VAL SER ASP TYR LYS MET LYS GLY SER VAL ASP LEU ILE SEQRES 7 B 337 VAL HIS TYR GLY HIS THR PRO LEU PRO LEU LYS TYR GLU SEQRES 8 B 337 VAL PRO THR LEU PHE ILE GLU ALA PHE SER ASN ILE ASP SEQRES 9 B 337 VAL LYS LYS ASP LEU GLU LYS CYS LEU GLU LYS LEU GLU SEQRES 10 B 337 ASP TYR SER LYS ILE ALA LEU VAL THR THR THR GLN HIS SEQRES 11 B 337 LEU HIS LEU LEU ASN GLU ILE LYS ASP TYR LEU GLU ASP SEQRES 12 B 337 ASN GLY LYS GLU VAL VAL LEU GLY SER SER LYS ASN THR SEQRES 13 B 337 LYS LYS GLY GLN VAL LEU GLY CYS ASN PHE SER SER ILE SEQRES 14 B 337 LYS ASN LEU ASP ALA GLU VAL TYR LEU PHE ILE GLY SER SEQRES 15 B 337 GLY ASN PHE HIS PRO LEU GLY ILE TYR LEU PHE THR LYS SEQRES 16 B 337 SER PRO VAL LEU ALA LEU ASP PRO TYR ASN SER GLU ILE SEQRES 17 B 337 ARG ASP ILE SER ALA PHE ALA ASP ARG ILE LEU ARG ILE SEQRES 18 B 337 ARG PHE ALA ARG ILE THR LYS ALA ARG GLU ALA GLU LYS SEQRES 19 B 337 TRP GLY ILE ILE VAL SER SER LYS GLU GLY GLN TYR ARG SEQRES 20 B 337 MET LYS LEU ALA LYS GLU ILE LYS LYS ILE LEU GLU ASP SEQRES 21 B 337 ASN LYS MET GLU ALA TYR ILE ILE MET ALA ASP ASN ILE SEQRES 22 B 337 ASN PRO ASP ILE LEU LEU PRO TYR MET GLU LEU ASP ALA SEQRES 23 B 337 PHE VAL VAL SER ALA CYS PRO ARG ILE ALA ILE ASP ASP SEQRES 24 B 337 SER GLN MET TYR LYS LYS PRO LEU LEU THR PRO GLN GLU SEQRES 25 B 337 LEU GLU ILE VAL LEU ASN LYS ARG GLN TRP GLU ASN TYR SEQRES 26 B 337 GLN LEU ASP GLU ILE LEU PHE HIS GLU ARG TYR LYS HET MTA A 401 20 HET SF4 A 402 8 HET CL A 403 1 HET MTA B 401 20 HET SF4 B 402 8 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CL CHLORIDE ION FORMUL 3 MTA 2(C11 H15 N5 O3 S) FORMUL 4 SF4 2(FE4 S4) FORMUL 5 CL CL 1- FORMUL 8 HOH *565(H2 O) HELIX 1 AA1 ASP A 7 GLY A 19 1 13 HELIX 2 AA2 PRO A 28 MET A 33 5 6 HELIX 3 AA3 GLN A 34 THR A 46 1 13 HELIX 4 AA4 SER A 64 LYS A 69 1 6 HELIX 5 AA5 VAL A 102 LYS A 104 5 3 HELIX 6 AA6 ASP A 105 LEU A 113 1 9 HELIX 7 AA7 THR A 125 HIS A 129 5 5 HELIX 8 AA8 LEU A 130 ASN A 141 1 12 HELIX 9 AA9 PHE A 163 LYS A 167 5 5 HELIX 10 AB1 ASN A 181 LYS A 192 1 12 HELIX 11 AB2 ILE A 208 ARG A 227 1 20 HELIX 12 AB3 LYS A 239 TYR A 243 5 5 HELIX 13 AB4 ARG A 244 ASN A 258 1 15 HELIX 14 AB5 ASN A 271 LEU A 276 1 6 HELIX 15 AB6 PRO A 290 ASP A 296 1 7 HELIX 16 AB7 SER A 297 TYR A 300 5 4 HELIX 17 AB8 THR A 306 LEU A 314 1 9 HELIX 18 AB9 GLN A 318 TYR A 322 5 5 HELIX 19 AC1 ASP B 7 GLY B 19 1 13 HELIX 20 AC2 PRO B 28 MET B 33 5 6 HELIX 21 AC3 GLN B 34 THR B 46 1 13 HELIX 22 AC4 GLY B 59 VAL B 63 5 5 HELIX 23 AC5 ASP B 101 LYS B 104 5 4 HELIX 24 AC6 ASP B 105 LEU B 113 1 9 HELIX 25 AC7 THR B 125 HIS B 129 5 5 HELIX 26 AC8 LEU B 130 ASN B 141 1 12 HELIX 27 AC9 PHE B 163 LYS B 167 5 5 HELIX 28 AD1 ASN B 181 LYS B 192 1 12 HELIX 29 AD2 ASP B 207 ARG B 227 1 21 HELIX 30 AD3 LYS B 239 TYR B 243 5 5 HELIX 31 AD4 ARG B 244 ASN B 258 1 15 HELIX 32 AD5 ASN B 271 LEU B 276 5 6 HELIX 33 AD6 PRO B 290 ASP B 296 1 7 HELIX 34 AD7 SER B 297 TYR B 300 5 4 HELIX 35 AD8 THR B 306 LEU B 314 1 9 HELIX 36 AD9 GLN B 318 TYR B 322 5 5 SHEET 1 AA1 8 THR A 91 ILE A 94 0 SHEET 2 AA1 8 LEU A 74 TYR A 78 1 N ILE A 75 O LEU A 92 SHEET 3 AA1 8 THR A 22 GLN A 26 1 N GLY A 24 O LEU A 74 SHEET 4 AA1 8 THR A 49 SER A 53 1 O SER A 53 N LEU A 25 SHEET 5 AA1 8 GLU B 261 ALA B 267 1 O MET B 266 N ILE A 52 SHEET 6 AA1 8 LYS B 231 SER B 237 1 N VAL B 236 O ILE B 265 SHEET 7 AA1 8 ALA B 283 VAL B 286 1 O VAL B 285 N ILE B 235 SHEET 8 AA1 8 LEU B 304 LEU B 305 1 O LEU B 305 N VAL B 286 SHEET 1 AA2 5 GLU A 144 VAL A 146 0 SHEET 2 AA2 5 LYS A 118 THR A 123 1 N ILE A 119 O GLU A 144 SHEET 3 AA2 5 VAL A 173 ILE A 177 1 O LEU A 175 N ALA A 120 SHEET 4 AA2 5 VAL A 195 ASP A 199 1 O LEU A 196 N PHE A 176 SHEET 5 AA2 5 GLU A 204 ASP A 207 -1 O GLU A 204 N ASP A 199 SHEET 1 AA3 8 LEU A 304 LEU A 305 0 SHEET 2 AA3 8 ALA A 283 VAL A 286 1 N VAL A 286 O LEU A 305 SHEET 3 AA3 8 LYS A 231 SER A 237 1 N ILE A 235 O VAL A 285 SHEET 4 AA3 8 GLU A 261 ALA A 267 1 O ILE A 265 N VAL A 236 SHEET 5 AA3 8 THR B 49 SER B 53 1 O ILE B 52 N ILE A 264 SHEET 6 AA3 8 THR B 22 GLN B 26 1 N VAL B 23 O ILE B 51 SHEET 7 AA3 8 LEU B 74 TYR B 78 1 O LEU B 74 N GLY B 24 SHEET 8 AA3 8 THR B 91 ILE B 94 1 O LEU B 92 N ILE B 75 SHEET 1 AA4 5 GLU B 144 VAL B 146 0 SHEET 2 AA4 5 LYS B 118 THR B 123 1 N ILE B 119 O GLU B 144 SHEET 3 AA4 5 VAL B 173 ILE B 177 1 O LEU B 175 N ALA B 120 SHEET 4 AA4 5 VAL B 195 LEU B 198 1 O LEU B 196 N PHE B 176 SHEET 5 AA4 5 ILE B 205 ARG B 206 -1 O ARG B 206 N ALA B 197 LINK SG CYS A 61 FE1 SF4 A 402 1555 1555 2.31 LINK SG CYS A 161 FE2 SF4 A 402 1555 1555 2.32 LINK SG CYS A 289 FE3 SF4 A 402 1555 1555 2.28 LINK SG CYS B 61 FE1 SF4 B 402 1555 1555 2.30 LINK SG CYS B 161 FE2 SF4 B 402 1555 1555 2.08 LINK SG CYS B 289 FE3 SF4 B 402 1555 1555 2.20 SITE 1 AC1 12 PHE A 58 LYS A 239 GLN A 242 ASP A 268 SITE 2 AC1 12 ASN A 269 ILE A 270 CYS A 289 ARG A 291 SITE 3 AC1 12 ASP A 295 ASP A 296 HOH A 568 HOH A 702 SITE 1 AC2 5 PHE A 58 CYS A 61 GLY A 160 CYS A 161 SITE 2 AC2 5 CYS A 289 SITE 1 AC3 3 MET A 245 LYS A 246 HOH A 788 SITE 1 AC4 13 PHE B 58 SER B 237 LYS B 239 GLN B 242 SITE 2 AC4 13 ASP B 268 ASN B 269 ILE B 270 CYS B 289 SITE 3 AC4 13 ARG B 291 ILE B 292 ASP B 295 ASP B 296 SITE 4 AC4 13 HOH B 607 SITE 1 AC5 5 PHE B 58 CYS B 61 GLY B 160 CYS B 161 SITE 2 AC5 5 CYS B 289 CRYST1 63.082 81.020 130.972 90.00 90.00 90.00 P 21 21 21 8 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 0.015852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007635 0.00000