10 20 30 40 50 60 70 80 3KAP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 19-OCT-09 3KAP
TITLE FLAVODOXIN FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 TITLE 2 (OXIDIZED FORM)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO DESULFURICANS SUBSP. SOURCE 3 DESULFURICANS STR. ATCC 27774; SOURCE 4 ORGANISM_TAXID: 525146; SOURCE 5 STRAIN: ATCC 27774 / DSM 6949
KEYWDS FLAVODOXIN, SULFATE-REDUCING BACTERIA, ELECTRON TRANSPORT, KEYWDS 2 FLAVOPROTEIN, FMN, TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR A.ROMERO,J.CALDEIRA,J.LEGALL,I.MOURA,J.J.G.MOURA,M.J.ROMAO
REVDAT 1 24-NOV-09 3KAP 0
JRNL AUTH A.ROMERO,J.CALDEIRA,J.LEGALL,I.MOURA,J.J.G.MOURA, JRNL AUTH 2 M.J.ROMAO JRNL TITL CRYSTAL STRUCTURE OF FLAVODOXIN FROM DESULFOVIBRIO JRNL TITL 2 DESULFURICANS ATCC 27774 IN TWO OXIDATION STATES JRNL REF EUR.J.BIOCHEM. V. 239 190 1996 JRNL REFN ISSN 0014-2956 JRNL PMID 8706707
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 0 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 0 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 92 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 2.93 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.94 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.25 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3KAP COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055758.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 5.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 180 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10938 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1FX1 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED AT ROOM REMARK 280 TEMPERATURE FROM A PROTEIN SOLUTION OF 8-10MG/ML IN A SOLUTION REMARK 280 CONTAINING 10% MPD, 2.3M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE (PH 5.0), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.46667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.23333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.23333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.46667 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2 OG REMARK 470 ASP A 44 CG OD1 OD2 REMARK 470 GLU A 63 CG CD OE1 OE2 REMARK 470 GLU A 122 CG CD OE1 OE2
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 HIS A 100 NE2 HIS A 100 CD2 -0.070 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 TRP A 60 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 60 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP A 60 CG - CD2 - CE3 ANGL. DEV. = 5.5 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 MET A 62 -101.73 50.88 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 150
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KAQ RELATED DB: PDB
DBREF 3KAP A 2 148 UNP P80312 FLAW_DESDA 2 148
SEQRES 1 A 147 SER LYS VAL LEU ILE LEU PHE GLY SER SER THR GLY ASN SEQRES 2 A 147 THR GLU SER ILE ALA GLN LYS LEU GLU GLU LEU VAL ALA SEQRES 3 A 147 ALA GLY GLY HIS GLU VAL THR LEU LEU ASN ALA ALA GLU SEQRES 4 A 147 ALA SER ALA ASP ASN LEU ALA ASP GLY TYR ASP ALA VAL SEQRES 5 A 147 LEU MET GLY CYS SER ALA TRP GLY MET GLU ASP LEU GLU SEQRES 6 A 147 LEU GLN ASP ASP PHE ALA PRO LEU PHE ASP GLU MET GLU SEQRES 7 A 147 ASN MET GLY LEU LYS GLY LYS LYS LEU ALA ALA PHE ALA SEQRES 8 A 147 SER GLY ASP MET GLU TYR GLU HIS TYR CYS GLY ALA VAL SEQRES 9 A 147 PRO ALA ILE GLU GLU LYS ALA ARG GLY LEU GLY ALA GLU SEQRES 10 A 147 VAL ILE CYS GLU GLY LEU LYS ILE GLU GLY ASP ALA SER SEQRES 11 A 147 SER ASP PRO ASP ALA VAL SER ALA PHE ALA GLU ASP VAL SEQRES 12 A 147 LEU LYS LYS LEU
HET FMN A 150 31
HETNAM FMN FLAVIN MONONUCLEOTIDE
HETSYN FMN RIBOFLAVIN MONOPHOSPHATE
FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *92(H2 O)
HELIX 1 1 GLY A 13 GLY A 29 1 17 HELIX 2 2 ALA A 39 ALA A 41 5 3 HELIX 3 3 PHE A 71 GLU A 77 1 7 HELIX 4 4 MET A 78 MET A 81 5 4 HELIX 5 5 GLY A 103 LEU A 115 1 13 HELIX 6 6 ASP A 129 SER A 132 5 4 HELIX 7 7 ASP A 133 LEU A 148 1 16
SHEET 1 A 5 GLU A 32 ASN A 37 0 SHEET 2 A 5 LYS A 3 GLY A 9 1 N VAL A 4 O GLU A 32 SHEET 3 A 5 ALA A 52 CYS A 57 1 O LEU A 54 N LEU A 5 SHEET 4 A 5 LYS A 87 GLY A 94 1 O ALA A 89 N MET A 55 SHEET 5 A 5 GLU A 118 VAL A 119 1 O GLU A 118 N LEU A 88 SHEET 1 B 5 GLU A 32 ASN A 37 0 SHEET 2 B 5 LYS A 3 GLY A 9 1 N VAL A 4 O GLU A 32 SHEET 3 B 5 ALA A 52 CYS A 57 1 O LEU A 54 N LEU A 5 SHEET 4 B 5 LYS A 87 GLY A 94 1 O ALA A 89 N MET A 55 SHEET 5 B 5 LEU A 124 GLU A 127 1 O LEU A 124 N ALA A 90
SITE 1 AC1 23 SER A 10 SER A 11 THR A 12 GLY A 13 SITE 2 AC1 23 ASN A 14 THR A 15 SER A 58 ALA A 59 SITE 3 AC1 23 TRP A 60 MET A 62 SER A 93 GLY A 94 SITE 4 AC1 23 ASP A 95 MET A 96 GLU A 97 TYR A 98 SITE 5 AC1 23 GLU A 99 HIS A 100 TYR A 101 CYS A 102 SITE 6 AC1 23 HOH A 306 HOH A 310 HOH A 391
CRYST1 95.900 95.900 33.700 90.00 90.00 120.00 P 32 2 1 6
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 0.010428 0.006020 0.000000 0.00000
SCALE2 0.000000 0.012041 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029674 0.00000