HEADER ELECTRON TRANSPORT 22-DEC-05 2FGO TITLE STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K38/PGP1-2; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS FERREDOXIN, PSEUDOMONAS AERUGINOSA, ALLOCHROMATIUM VINOSUM, [4FE-4S] KEYWDS 2 CLUSTER, REDUCTION POTENTIAL, IRON BINDING PROTEIN, ELECTRON KEYWDS 3 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR P.GIASTAS,N.PINOTSIS,I.M.MAVRIDIS REVDAT 4 30-AUG-23 2FGO 1 REMARK LINK REVDAT 3 24-FEB-09 2FGO 1 VERSN REVDAT 2 23-MAY-06 2FGO 1 JRNL REVDAT 1 18-APR-06 2FGO 0 JRNL AUTH P.GIASTAS,N.PINOTSIS,G.EFTHYMIOU,M.WILMANNS,P.KYRITSIS, JRNL AUTH 2 J.-M.MOULIS,I.M.MAVRIDIS JRNL TITL THE STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM PSEUDOMONAS JRNL TITL 2 AERUGINOSA AT 1.32-A RESOLUTION: COMPARISON WITH OTHER JRNL TITL 3 HIGH-RESOLUTION STRUCTURES OF FERREDOXINS AND CONTRIBUTING JRNL TITL 4 STRUCTURAL FEATURES TO REDUCTION POTENTIAL VALUES. JRNL REF J.BIOL.INORG.CHEM. V. 11 445 2006 JRNL REFN ISSN 0949-8257 JRNL PMID 16596388 JRNL DOI 10.1007/S00775-006-0094-9 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.176 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 20405 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.152 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 15657 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 622 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 759.75 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6462 REMARK 3 NUMBER OF RESTRAINTS : 1944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.350 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.050 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.085 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.030 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8414 REMARK 200 MONOCHROMATOR : TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : 0.37300 REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 1BLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M (NH4)2HPO4, 0.230M NACL, PH 7.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, PH 7.40 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 19.54350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.97650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.56450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.97650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.54350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.56450 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 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 ALA A 82 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 ASP A 12 -8.03 75.71 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 201 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 SF4 A 201 S2 117.5 REMARK 620 3 SF4 A 201 S3 118.7 104.9 REMARK 620 4 SF4 A 201 S4 105.4 105.9 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 SF4 A 201 S1 103.6 REMARK 620 3 SF4 A 201 S3 120.3 104.2 REMARK 620 4 SF4 A 201 S4 119.8 102.9 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 SF4 A 201 S1 109.2 REMARK 620 3 SF4 A 201 S2 119.6 103.9 REMARK 620 4 SF4 A 201 S4 112.3 104.1 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 202 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 SF4 A 202 S1 112.5 REMARK 620 3 SF4 A 202 S2 118.8 102.9 REMARK 620 4 SF4 A 202 S3 106.8 109.0 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 202 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 37 SG REMARK 620 2 SF4 A 202 S2 113.1 REMARK 620 3 SF4 A 202 S3 118.2 106.1 REMARK 620 4 SF4 A 202 S4 109.4 106.0 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 202 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 40 SG REMARK 620 2 SF4 A 202 S1 96.1 REMARK 620 3 SF4 A 202 S3 122.7 106.1 REMARK 620 4 SF4 A 202 S4 123.7 103.3 101.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 202 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 SF4 A 202 S1 111.5 REMARK 620 3 SF4 A 202 S2 123.3 102.8 REMARK 620 4 SF4 A 202 S4 107.4 105.2 105.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 201 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 53 SG REMARK 620 2 SF4 A 201 S1 109.7 REMARK 620 3 SF4 A 201 S2 124.1 101.3 REMARK 620 4 SF4 A 201 S3 114.0 101.5 103.4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 202 DBREF 2FGO A 1 82 UNP Q9I6D2 Q9I6D2_PSEAE 2 83 SEQRES 1 A 82 SER LEU LYS ILE THR ASP ASP CYS ILE ASN CYS ASP VAL SEQRES 2 A 82 CYS GLU PRO GLU CYS PRO ASN GLY ALA ILE SER GLN GLY SEQRES 3 A 82 GLU GLU ILE TYR VAL ILE ASP PRO ASN LEU CYS THR GLU SEQRES 4 A 82 CYS VAL GLY HIS TYR ASP GLU PRO GLN CYS GLN GLN VAL SEQRES 5 A 82 CYS PRO VAL ASP CYS ILE PRO LEU ASP ASP ALA ASN VAL SEQRES 6 A 82 GLU SER LYS ASP GLN LEU MET GLU LYS TYR ARG LYS ILE SEQRES 7 A 82 THR GLY LYS ALA HET SF4 A 201 8 HET SF4 A 202 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 2(FE4 S4) FORMUL 4 HOH *141(H2 O) HELIX 1 1 CYS A 14 CYS A 18 5 5 HELIX 2 2 PRO A 47 CYS A 53 1 7 HELIX 3 3 SER A 67 GLY A 80 1 14 SHEET 1 A 2 ILE A 23 GLN A 25 0 SHEET 2 A 2 TYR A 30 ILE A 32 -1 O VAL A 31 N SER A 24 LINK SG CYS A 8 FE1 SF4 A 201 1555 1555 2.30 LINK SG CYS A 11 FE2 SF4 A 201 1555 1555 2.24 LINK SG CYS A 14 FE3 SF4 A 201 1555 1555 2.26 LINK SG CYS A 18 FE4 SF4 A 202 1555 1555 2.32 LINK SG CYS A 37 FE1 SF4 A 202 1555 1555 2.32 LINK SG CYS A 40 FE2 SF4 A 202 1555 1555 2.26 LINK SG CYS A 49 FE3 SF4 A 202 1555 1555 2.27 LINK SG CYS A 53 FE4 SF4 A 201 1555 1555 2.32 SITE 1 AC1 9 CYS A 8 ILE A 9 CYS A 11 ASP A 12 SITE 2 AC1 9 VAL A 13 CYS A 14 TYR A 30 CYS A 53 SITE 3 AC1 9 CYS A 57 SITE 1 AC2 8 LEU A 2 CYS A 18 CYS A 37 THR A 38 SITE 2 AC2 8 GLU A 39 CYS A 40 PRO A 47 CYS A 49 CRYST1 39.087 45.129 51.953 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 0.025584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019248 0.00000