HEADER ELECTRON TRANSPORT 22-MAR-23 8ITO TITLE CRYSTAL STRUCTURE OF FERLP FROM DESULFOVIBRIO VULGARIS (HILDENBOROUGH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 882; SOURCE 4 STRAIN: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / SOURCE 5 HILDENBOROUGH; SOURCE 6 GENE: RDL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS IRON-SULFUR CLUSTER, METALLO PROTEIN, MONOMER, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKATSUJI,H.OGATA,M.KITAMURA REVDAT 2 23-OCT-24 8ITO 1 REMARK REVDAT 1 27-MAR-24 8ITO 0 JRNL AUTH T.NAKATSUJI,K.NISHIKAWA,H.OGATA,M.KITAMURA JRNL TITL CRYSTAL STRUCTURE OF FERLP FROM DESULFOVIBRIO VULGARIS JRNL TITL 2 (HILDENBOROUGH) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 7606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.060 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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 18.6800 - 3.0300 0.99 2477 168 0.1574 0.2036 REMARK 3 2 3.0300 - 2.4000 1.00 2402 146 0.2149 0.2836 REMARK 3 3 2.4000 - 2.1000 0.96 2266 147 0.2498 0.3627 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.500 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 : 0.008 1203 REMARK 3 ANGLE : 0.991 1633 REMARK 3 CHIRALITY : 0.058 157 REMARK 3 PLANARITY : 0.011 223 REMARK 3 DIHEDRAL : 6.061 161 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 8ITO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52024 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 18.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M NAHPO4, 0.9 M K2HPO4, 0.8 M REMARK 280 POTASSIUM SODIUM TARTRATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 18.28250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.59900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.92800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.59900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.28250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.92800 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 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 MET A 1 REMARK 465 LYS A 75 REMARK 465 MET B 1 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 O GLU B 37 O HOH B 201 2.16 REMARK 500 O HOH A 226 O HOH A 227 2.19 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 CYS A 15 -143.20 -106.03 REMARK 500 THR A 73 -141.89 -137.93 REMARK 500 CYS B 15 -116.66 -107.86 REMARK 500 PRO B 40 155.70 -49.78 REMARK 500 CYS B 69 -167.44 -163.52 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 102 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 10 SG REMARK 620 2 CYS A 15 SG 111.7 REMARK 620 3 CYS A 45 SG 113.5 103.7 REMARK 620 4 CYS A 48 SG 99.3 115.4 113.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 102 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 10 SG REMARK 620 2 CYS B 15 SG 111.7 REMARK 620 3 CYS B 45 SG 115.2 105.9 REMARK 620 4 CYS B 48 SG 97.6 118.8 108.0 REMARK 620 N 1 2 3 DBREF 8ITO A 1 75 UNP Q726L3 Q726L3_DESVH 1 75 DBREF 8ITO B 1 75 UNP Q726L3 Q726L3_DESVH 1 75 SEQRES 1 A 75 MET ALA ASN PRO GLU ASP MET TRP ARG CYS GLN THR VAL SEQRES 2 A 75 ASN CYS GLY TYR VAL TYR ASP PRO ASP ARG GLY ASP LYS SEQRES 3 A 75 ARG GLY LYS VAL PRO PRO GLY THR ARG PHE GLU ASP LEU SEQRES 4 A 75 PRO ASP GLU TRP ARG CYS PRO ILE CYS LYS ALA THR LYS SEQRES 5 A 75 LYS CYS PHE ARG PRO LEU ALA GLY PRO GLY SER THR GLU SEQRES 6 A 75 GLN PRO GLN CYS GLU MET PRO THR ASP LYS SEQRES 1 B 75 MET ALA ASN PRO GLU ASP MET TRP ARG CYS GLN THR VAL SEQRES 2 B 75 ASN CYS GLY TYR VAL TYR ASP PRO ASP ARG GLY ASP LYS SEQRES 3 B 75 ARG GLY LYS VAL PRO PRO GLY THR ARG PHE GLU ASP LEU SEQRES 4 B 75 PRO ASP GLU TRP ARG CYS PRO ILE CYS LYS ALA THR LYS SEQRES 5 B 75 LYS CYS PHE ARG PRO LEU ALA GLY PRO GLY SER THR GLU SEQRES 6 B 75 GLN PRO GLN CYS GLU MET PRO THR ASP LYS HET PO4 A 101 5 HET FE A 102 1 HET PO4 B 101 5 HET FE B 102 1 HETNAM PO4 PHOSPHATE ION HETNAM FE FE (III) ION FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 FE 2(FE 3+) FORMUL 7 HOH *67(H2 O) HELIX 1 AA1 ASN A 3 ASP A 6 5 4 HELIX 2 AA2 ARG A 35 LEU A 39 5 5 HELIX 3 AA3 THR A 51 LYS A 53 5 3 HELIX 4 AA4 GLY A 60 GLU A 65 5 6 HELIX 5 AA5 ASN B 3 ASP B 6 5 4 HELIX 6 AA6 ARG B 35 LEU B 39 5 5 HELIX 7 AA7 THR B 51 LYS B 53 5 3 SHEET 1 AA1 3 VAL A 18 TYR A 19 0 SHEET 2 AA1 3 TRP A 8 CYS A 10 -1 N TRP A 8 O TYR A 19 SHEET 3 AA1 3 PHE A 55 PRO A 57 -1 O ARG A 56 N ARG A 9 SHEET 1 AA2 3 VAL B 18 TYR B 19 0 SHEET 2 AA2 3 TRP B 8 CYS B 10 -1 N TRP B 8 O TYR B 19 SHEET 3 AA2 3 PHE B 55 PRO B 57 -1 O ARG B 56 N ARG B 9 SSBOND 1 CYS A 54 CYS A 69 1555 1555 2.04 SSBOND 2 CYS B 54 CYS B 69 1555 1555 2.04 LINK SG CYS A 10 FE FE A 102 1555 1555 2.36 LINK SG CYS A 15 FE FE A 102 1555 1555 2.39 LINK SG CYS A 45 FE FE A 102 1555 1555 2.36 LINK SG CYS A 48 FE FE A 102 1555 1555 2.25 LINK SG CYS B 10 FE FE B 102 1555 1555 2.34 LINK SG CYS B 15 FE FE B 102 1555 1555 2.25 LINK SG CYS B 45 FE FE B 102 1555 1555 2.38 LINK SG CYS B 48 FE FE B 102 1555 1555 2.33 CRYST1 36.565 57.856 59.198 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 0.027349 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016892 0.00000