HEADER BIOSYNTHETIC PROTEIN 25-AUG-25 9WGR TITLE E. COLI SUFE WITH DELETION OF TQHL (RESIDUES 112-115) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE DESULFURATION PROTEIN SUFE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: SUFE, YNHA, B1679, JW1669; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS SULFUR TRANSFERASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.SAKURAI,T.FUJISHIRO REVDAT 1 02-SEP-26 9WGR 0 JRNL AUTH R.SAKURAI,N.YOKOYAMA,Y.TAKAHASHI,T.FUJISHIRO JRNL TITL STRUCTURAL EVOLUTION OF SULFUR TRANSFER SYSTEMS IN FE-S JRNL TITL 2 CLUSTER BIOSYNTHESIS SUF SYSTEMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1188 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 27.9000 - 3.0600 1.00 2955 155 0.1839 0.1848 REMARK 3 2 3.0600 - 2.4300 1.00 2838 150 0.1907 0.1946 REMARK 3 3 2.4300 - 2.1200 1.00 2824 148 0.1760 0.1771 REMARK 3 4 2.1200 - 1.9300 1.00 2800 148 0.1761 0.2031 REMARK 3 5 1.9300 - 1.7900 1.00 2802 147 0.1836 0.2078 REMARK 3 6 1.7900 - 1.6800 1.00 2783 147 0.1828 0.2201 REMARK 3 7 1.6800 - 1.6000 1.00 2785 146 0.1722 0.2008 REMARK 3 8 1.6000 - 1.5300 1.00 2798 147 0.1785 0.1977 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.125 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.872 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.96 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 : 0.006 1112 REMARK 3 ANGLE : 0.796 1506 REMARK 3 CHIRALITY : 0.050 164 REMARK 3 PLANARITY : 0.009 193 REMARK 3 DIHEDRAL : 16.945 420 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9WGR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300063002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23780 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 27.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3M MES-NAOH, 0.3M LITHIUM SULFATE, REMARK 280 15% (W/V) PEG 4000, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.80500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.80500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.80500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.90000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.80500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.80500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.90000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.80500 REMARK 290 SMTRY3 8 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: 180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 ALA A 2 REMARK 465 ALA A 137 REMARK 465 LEU A 138 REMARK 465 GLU A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 DBREF 9WGR A 1 134 UNP P76194 SUFE_ECOLI 1 138 SEQADV 9WGR A UNP P76194 THR 112 DELETION SEQADV 9WGR A UNP P76194 GLN 113 DELETION SEQADV 9WGR A UNP P76194 HIS 114 DELETION SEQADV 9WGR A UNP P76194 LEU 115 DELETION SEQADV 9WGR TRP A 135 UNP P76194 EXPRESSION TAG SEQADV 9WGR ALA A 136 UNP P76194 EXPRESSION TAG SEQADV 9WGR ALA A 137 UNP P76194 EXPRESSION TAG SEQADV 9WGR LEU A 138 UNP P76194 EXPRESSION TAG SEQADV 9WGR GLU A 139 UNP P76194 EXPRESSION TAG SEQADV 9WGR HIS A 140 UNP P76194 EXPRESSION TAG SEQADV 9WGR HIS A 141 UNP P76194 EXPRESSION TAG SEQADV 9WGR HIS A 142 UNP P76194 EXPRESSION TAG SEQADV 9WGR HIS A 143 UNP P76194 EXPRESSION TAG SEQADV 9WGR HIS A 144 UNP P76194 EXPRESSION TAG SEQADV 9WGR HIS A 145 UNP P76194 EXPRESSION TAG SEQRES 1 A 145 MET ALA LEU LEU PRO ASP LYS GLU LYS LEU LEU ARG ASN SEQRES 2 A 145 PHE LEU ARG CYS ALA ASN TRP GLU GLU LYS TYR LEU TYR SEQRES 3 A 145 ILE ILE GLU LEU GLY GLN ARG LEU PRO GLU LEU ARG ASP SEQRES 4 A 145 GLU ASP ARG SER PRO GLN ASN SER ILE GLN GLY CYS GLN SEQRES 5 A 145 SER GLN VAL TRP ILE VAL MET ARG GLN ASN ALA GLN GLY SEQRES 6 A 145 ILE ILE GLU LEU GLN GLY ASP SER ASP ALA ALA ILE VAL SEQRES 7 A 145 LYS GLY LEU ILE ALA VAL VAL PHE ILE LEU TYR ASP GLN SEQRES 8 A 145 MET THR PRO GLN ASP ILE VAL ASN PHE ASP VAL ARG PRO SEQRES 9 A 145 TRP PHE GLU LYS MET ALA LEU THR PRO SER ARG SER GLN SEQRES 10 A 145 GLY LEU GLU ALA MET ILE ARG ALA ILE ARG ALA LYS ALA SEQRES 11 A 145 ALA ALA LEU SER TRP ALA ALA LEU GLU HIS HIS HIS HIS SEQRES 12 A 145 HIS HIS HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *109(H2 O) HELIX 1 AA1 ASP A 6 ARG A 16 1 11 HELIX 2 AA2 ASN A 19 ARG A 33 1 15 HELIX 3 AA3 ARG A 38 ARG A 42 5 5 HELIX 4 AA4 SER A 43 SER A 47 5 5 HELIX 5 AA5 ALA A 75 TYR A 89 1 15 HELIX 6 AA6 THR A 93 PHE A 100 1 8 HELIX 7 AA7 VAL A 102 ALA A 110 1 9 HELIX 8 AA8 SER A 116 TRP A 135 1 20 SHEET 1 AA1 2 VAL A 55 GLN A 61 0 SHEET 2 AA1 2 ILE A 67 SER A 73 -1 O GLN A 70 N VAL A 58 CRYST1 55.800 79.610 69.610 90.00 90.00 90.00 C 2 2 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 0.017921 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014366 0.00000 CONECT 1082 1083 1084 1085 1086 CONECT 1083 1082 CONECT 1084 1082 CONECT 1085 1082 CONECT 1086 1082 CONECT 1087 1088 1089 1090 1091 CONECT 1088 1087 CONECT 1089 1087 CONECT 1090 1087 CONECT 1091 1087 CONECT 1092 1093 1094 1095 1096 CONECT 1093 1092 CONECT 1094 1092 CONECT 1095 1092 CONECT 1096 1092 MASTER 236 0 3 8 2 0 0 6 1204 1 15 12 END