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- PDB-1xt6: S35C Flavodoxin Mutant in the semiquinone state -

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Basic information

Entry
Database: PDB / ID: 1xt6
TitleS35C Flavodoxin Mutant in the semiquinone state
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / PROTEIN / FLAVODOXIN / MUTANT / S35C
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold ...Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris subsp. vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArtali, R. / Marchini, N. / Meneghetti, F. / Cavazzini, D. / Cassetta, A. / Sassone, C. / Bombieri, G. / Rossi, G.L. / Gilardi, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of S35C flavodoxin mutant from Desulfovibrio vulgaris in the semiquinone state.
Authors: Artali, R. / Marchini, N. / Meneghetti, F. / Cavazzini, D. / Cassetta, A. / Sassone, C.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1512
Polymers15,6941
Non-polymers4561
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.080, 51.080, 138.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Flavodoxin /


Mass: 15694.174 Da / Num. of mol.: 1 / Mutation: S35C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris (bacteria)
Species: Desulfovibrio vulgaris / Strain: Hildenborough / Production host: Desulfovibrio vulgaris (bacteria) / Keywords: polypeptide / References: UniProt: P00323
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 298 K / Method: sitting drop, vapor diffusion / pH: 7
Details: 3.2M ammonium sulfate, pH 7, sitting drop, vapor diffusion, temperature 298K
Components of the solutionsConc.: 6-8 mg/ml / Name: protein in buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2003 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.4 Å / Num. obs: 14037 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.9 Å2
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.067 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1390983.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 20 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1361 9.7 %RANDOM
Rwork0.192 ---
all0.261 17132 --
obs0.192 14037 79.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.2532 Å2 / ksol: 0.495598 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å20 Å20 Å2
2--4.21 Å20 Å2
3----8.43 Å2
Refine Biso Class: all / Treatment: anisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 31 128 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.063
X-RAY DIFFRACTIONc_angle_deg4.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d4.05
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.652
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 109 9.1 %
Rwork0.206 1089 -
obs--41.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FMN.PARAMFMN.TOP

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