HEADER ELECTRON TRANSPORT 27-MAR-97 1AKQ TITLE D95A OXIDIZED FLAVODOXIN MUTANT FROM D. VULGARIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: TG2 KEYWDS ELECTRON TRANSPORT, ELECTRON TRANSFER, FLAVOPROTEIN, FMN, FLAVODOXIN, KEYWDS 2 MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR A.MCCARTHY,M.WALSH,T.HIGGINS REVDAT 5 07-FEB-24 1AKQ 1 REMARK REVDAT 4 03-NOV-21 1AKQ 1 REMARK SEQADV REVDAT 3 24-FEB-09 1AKQ 1 VERSN REVDAT 2 01-APR-03 1AKQ 1 JRNL REVDAT 1 02-DEC-98 1AKQ 0 JRNL AUTH A.A.MCCARTHY,M.A.WALSH,C.S.VERMA,D.P.O'CONNELL,M.REINHOLD, JRNL AUTH 2 G.N.YALLOWAY,D.D'ARCY,T.M.HIGGINS,G.VOORDOUW,S.G.MAYHEW JRNL TITL CRYSTALLOGRAPHIC INVESTIGATION OF THE ROLE OF ASPARTATE 95 JRNL TITL 2 IN THE MODULATION OF THE REDOX POTENTIALS OF DESULFOVIBRIO JRNL TITL 3 VULGARIS FLAVODOXIN. JRNL REF BIOCHEMISTRY V. 41 10950 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12206666 JRNL DOI 10.1021/BI020225H REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17939 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 896 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1960 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1897 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 896 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17939 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.80 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.050 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.032 ; 0.040 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.140 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.180 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.252 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 1.811 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 17.100; 15.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AKQ 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_1000170937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL 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 : 17939 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.52000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 60-70% REMARK 280 A.S., 100MM TRIS-HCL, PH=7.0., PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 69.97400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.40250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.40250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.96100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.40250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.40250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.98700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.40250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.40250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 104.96100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.40250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.40250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.98700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.97400 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 230 O HOH A 238 4565 0.32 REMARK 500 O HOH A 245 O HOH A 248 6465 0.85 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 GLN A 121 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 131 NE - CZ - NH1 ANGL. DEV. = 3.2 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 62 -83.18 67.28 REMARK 500 TYR A 100 79.77 -104.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FMN REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: FMN CO-FACTOR. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 149 DBREF 1AKQ A 2 148 UNP P00323 FLAV_DESVH 2 148 SEQADV 1AKQ ALA A 95 UNP P00323 ASP 95 ENGINEERED MUTATION SEQRES 1 A 147 PRO LYS ALA LEU ILE VAL TYR GLY SER THR THR GLY ASN SEQRES 2 A 147 THR GLU TYR THR ALA GLU THR ILE ALA ARG GLU LEU ALA SEQRES 3 A 147 ASP ALA GLY TYR GLU VAL ASP SER ARG ASP ALA ALA SER SEQRES 4 A 147 VAL GLU ALA GLY GLY LEU PHE GLU GLY PHE ASP LEU VAL SEQRES 5 A 147 LEU LEU GLY CYS SER THR TRP GLY ASP ASP SER ILE GLU SEQRES 6 A 147 LEU GLN ASP ASP PHE ILE PRO LEU PHE ASP SER LEU GLU SEQRES 7 A 147 GLU THR GLY ALA GLN GLY ARG LYS VAL ALA CYS PHE GLY SEQRES 8 A 147 CYS GLY ALA SER SER TYR GLU TYR PHE CYS GLY ALA VAL SEQRES 9 A 147 ASP ALA ILE GLU GLU LYS LEU LYS ASN LEU GLY ALA GLU SEQRES 10 A 147 ILE VAL GLN ASP GLY LEU ARG ILE ASP GLY ASP PRO ARG SEQRES 11 A 147 ALA ALA ARG ASP ASP ILE VAL GLY TRP ALA HIS ASP VAL SEQRES 12 A 147 ARG GLY ALA ILE HET FMN A 149 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *100(H2 O) HELIX 1 1 ASN A 14 ASP A 28 1 15 HELIX 2 2 ALA A 38 SER A 40 5 3 HELIX 3 3 ILE A 72 GLU A 80 1 9 HELIX 4 4 GLY A 103 ASN A 114 1 12 HELIX 5 5 PRO A 130 ARG A 145 5 16 SHEET 1 A 5 GLU A 32 ASP A 37 0 SHEET 2 A 5 LYS A 3 GLY A 9 1 N ALA A 4 O GLU A 32 SHEET 3 A 5 LEU A 52 CYS A 57 1 N LEU A 52 O LEU A 5 SHEET 4 A 5 VAL A 88 GLY A 94 1 N ALA A 89 O VAL A 53 SHEET 5 A 5 LEU A 124 ASP A 127 1 N LEU A 124 O GLY A 92 SITE 1 FMN 1 FMN A 149 SITE 1 AC1 23 SER A 10 THR A 11 THR A 12 GLY A 13 SITE 2 AC1 23 ASN A 14 THR A 15 ALA A 27 ASP A 28 SITE 3 AC1 23 SER A 58 THR A 59 TRP A 60 ASP A 62 SITE 4 AC1 23 CYS A 93 GLY A 94 ALA A 95 TYR A 98 SITE 5 AC1 23 TYR A 100 PHE A 101 CYS A 102 HOH A 157 SITE 6 AC1 23 HOH A 158 HOH A 168 HOH A 182 CRYST1 52.805 52.805 139.948 90.00 90.00 90.00 P 43 21 2 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 0.018938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007146 0.00000