HEADER IRON-SULFUR PROTEIN 21-DEC-97 1RB9 TITLE RUBREDOXIN FROM DESULFOVIBRIO VULGARIS REFINED ANISOTROPICALLY AT 0.92 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. SOURCE 3 HILDENBOROUGH; SOURCE 4 ORGANISM_TAXID: 882; SOURCE 5 STRAIN: HILDENBOROUGH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IRON-SULFUR PROTEIN, RUBREDOXIN, ATOMIC RESOLUTION, ANISOTROPIC KEYWDS 2 REFINEMENT EXPDTA X-RAY DIFFRACTION AUTHOR Z.DAUTER,S.BUTTERWORTH,L.C.SIEKER,G.SHELDRICK,K.S.WILSON REVDAT 4 20-NOV-24 1RB9 1 REMARK REVDAT 3 09-AUG-23 1RB9 1 REMARK LINK REVDAT 2 24-FEB-09 1RB9 1 VERSN REVDAT 1 16-FEB-99 1RB9 0 JRNL AUTH Z.DAUTER,S.BUTTERWORTH,L.C.SIEKER,G.SHELDRICK,K.S.WILSON JRNL TITL ANISOTROPIC REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO JRNL TITL 2 VULGARIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.92 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) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 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) : 0.073 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) : 48061 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.071 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)) : 44545 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 391 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1426.6 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 524.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5037 REMARK 3 NUMBER OF RESTRAINTS : 5439 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 ANGLE DISTANCES (A) : 0.038 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.031 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.153 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.240 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.102 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FRIEDEL RELATED REFLECTIONS NOT MERGED REMARK 4 REMARK 4 1RB9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175986. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-88 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.5 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 : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.70 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AGROVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26124 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : 0.03100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.14800 REMARK 200 R SYM FOR SHELL (I) : 0.14800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MODEL KNOWN (8RXN) REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: 8RXN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 20.72500 REMARK 290 SMTRY3 2 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 50 CD GLU A 50 OE1 -0.076 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 2 CD - CE - NZ ANGL. DEV. = 21.2 DEGREES REMARK 500 GLU A 12 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP A 21 CB - CA - C ANGL. DEV. = 14.1 DEGREES 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 ASP A 19 75.74 -154.18 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 FE2 A 54 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 114.9 REMARK 620 3 CYS A 39 SG 110.5 104.3 REMARK 620 4 CYS A 42 SG 105.1 110.5 111.8 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 FE2 A 54 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 56 DBREF 1RB9 A 1 52 UNP P00269 RUBR_DESVH 1 52 SEQRES 1 A 52 FME LYS LYS TYR VAL CYS THR VAL CYS GLY TYR GLU TYR SEQRES 2 A 52 ASP PRO ALA GLU GLY ASP PRO ASP ASN GLY VAL LYS PRO SEQRES 3 A 52 GLY THR SER PHE ASP ASP LEU PRO ALA ASP TRP VAL CYS SEQRES 4 A 52 PRO VAL CYS GLY ALA PRO LYS SER GLU PHE GLU ALA ALA MODRES 1RB9 FME A 1 MET N-FORMYLMETHIONINE HET FME A 1 15 HET FE2 A 54 1 HET SO4 A 56 10 HETNAM FME N-FORMYLMETHIONINE HETNAM FE2 FE (II) ION HETNAM SO4 SULFATE ION FORMUL 1 FME C6 H11 N O3 S FORMUL 2 FE2 FE 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *93(H2 O) HELIX 1 1 PRO A 20 ASN A 22 5 3 HELIX 2 2 PHE A 30 ASP A 32 5 3 HELIX 3 3 SER A 47 GLU A 48 1 2 SHEET 1 A 2 TYR A 4 CYS A 6 0 SHEET 2 A 2 PHE A 49 ALA A 51 -1 N GLU A 50 O VAL A 5 SHEET 1 B 2 ALA A 44 GLU A 48 0 SHEET 2 B 2 PRO A 45 GLU A 48 1 N PRO A 45 O PRO A 45 LINK C AFME A 1 N LYS A 2 1555 1555 1.33 LINK C BFME A 1 N LYS A 2 1555 1555 1.28 LINK SG CYS A 6 FE FE2 A 54 1555 1555 2.28 LINK SG CYS A 9 FE FE2 A 54 1555 1555 2.27 LINK SG CYS A 39 FE FE2 A 54 1555 1555 2.29 LINK SG CYS A 42 FE FE2 A 54 1555 1555 2.24 SITE 1 AC1 4 CYS A 6 CYS A 9 CYS A 39 CYS A 42 SITE 1 AC2 13 LYS A 3 ALA A 35 TRP A 37 PRO A 45 SITE 2 AC2 13 LYS A 46 SER A 47 HOH A 85 HOH A 95 SITE 3 AC2 13 HOH A 96 HOH A 103 HOH A 125 HOH A 126 SITE 4 AC2 13 HOH A 146 CRYST1 19.970 41.450 24.410 90.00 108.30 90.00 P 1 21 1 2 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 0.050075 0.000000 0.016561 0.00000 SCALE2 0.000000 0.024125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043149 0.00000 HETATM 1 N FME A 1 -3.221 -14.910 -2.504 1.00 17.32 N ANISOU 1 N FME A 1 2145 1332 3105 -295 373 -319 N HETATM 2 CN FME A 1 -3.531 -15.743 -1.438 0.47 20.46 C ANISOU 2 CN FME A 1 2407 1915 3453 -900 463 44 C HETATM 3 O1 FME A 1 -3.145 -15.316 -0.326 0.47 24.95 O ANISOU 3 O1 FME A 1 2912 3335 3234 -1940 156 640 O HETATM 4 CA FME A 1 -1.996 -14.225 -2.678 1.00 14.18 C ANISOU 4 CA FME A 1 2055 962 2371 -266 504 -543 C HETATM 5 CB FME A 1 -1.116 -14.654 -3.808 1.00 14.31 C ANISOU 5 CB FME A 1 1879 1713 1846 359 132 -419 C HETATM 6 CG AFME A 1 -0.673 -16.082 -3.608 0.72 13.24 C ANISOU 6 CG AFME A 1 1331 1494 2206 -86 -175 -623 C HETATM 7 CG BFME A 1 -0.382 -16.063 -3.666 0.28 16.00 C ANISOU 7 CG BFME A 1 2461 1514 2105 332 -156 -961 C HETATM 8 SD AFME A 1 0.861 -15.983 -2.604 0.72 10.19 S ANISOU 8 SD AFME A 1 1389 1210 1275 -225 48 -395 S HETATM 9 SD BFME A 1 -0.538 -16.813 -1.996 0.28 31.25 S ANISOU 9 SD BFME A 1 6133 2416 3326 634 109 572 S HETATM 10 CE AFME A 1 0.678 -17.440 -1.553 0.72 20.52 C ANISOU 10 CE AFME A 1 3345 1559 2893 372 189 525 C HETATM 11 CE BFME A 1 1.007 -17.724 -1.846 0.28 18.09 C ANISOU 11 CE BFME A 1 4814 1433 625 -719 60 -76 C HETATM 12 C AFME A 1 -2.161 -12.718 -2.657 0.68 11.52 C ANISOU 12 C AFME A 1 1898 1100 1379 -245 268 -413 C HETATM 13 C BFME A 1 -2.597 -12.648 -3.267 0.32 13.35 C ANISOU 13 C BFME A 1 2121 1225 1728 -214 477 -402 C HETATM 14 O AFME A 1 -1.175 -12.018 -2.936 0.68 13.15 O ANISOU 14 O AFME A 1 2117 1054 1826 -360 415 -101 O HETATM 15 O BFME A 1 -2.384 -11.858 -4.206 0.32 17.74 O ANISOU 15 O BFME A 1 3415 1521 1805 -408 676 -235 O