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- PDB-6ft1: Crystal structure of oxidised Flavodoxin 1 from Bacillus cereus (... -

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Basic information

Entry
Database: PDB / ID: 6ft1
TitleCrystal structure of oxidised Flavodoxin 1 from Bacillus cereus (1.4 A resolution)
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / flavodoxin / electron transfer / FMN
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short chain / : / Flavodoxin domain / 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 / alpha-D-glucopyranose / Flavodoxin / Flavodoxin
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGudim, I. / Lofstad, M. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway231669 Norway
CitationJournal: Protein Sci. / Year: 2018
Title: High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus.
Authors: Gudim, I. / Lofstad, M. / van Beek, W. / Hersleth, H.P.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,8484
Polymers16,1151
Non-polymers7333
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-16 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.840, 44.860, 81.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Flavodoxin


Mass: 16115.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: ICO_01211 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R8KEI7, UniProt: Q81G35*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3.6 M ammonium sulfate and 0.1 M citric acid pH 4 (final pH 5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.70024 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70024 Å / Relative weight: 1
ReflectionResolution: 1.4→39.291 Å / Num. obs: 28302 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.039 / Rrim(I) all: 0.077 / Net I/σ(I): 15.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1382 / CC1/2: 0.671 / Rpim(I) all: 0.293 / Rrim(I) all: 0.524 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WSB

1wsb


Resolution: 1.4→39.291 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.43
RfactorNum. reflection% reflection
Rfree0.2045 1388 4.91 %
Rwork0.1775 --
obs0.1788 28277 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.56 Å2 / Biso mean: 14.5425 Å2 / Biso min: 5 Å2
Refinement stepCycle: final / Resolution: 1.4→39.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 48 178 1355
Biso mean--24.16 24.51 -
Num. residues----147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.45010.24441300.219226872817100
1.4501-1.50810.23551440.213526502794100
1.5081-1.57680.26531450.210226772822100
1.5768-1.65990.23831390.22462675281499
1.6599-1.76390.31541200.25082663278398
1.7639-1.90010.25551430.2322671281499
1.9001-2.09130.25541500.19772691284199
2.0913-2.39390.17051360.15452687282398
2.3939-3.01580.17451320.14652687281996
3.0158-39.30660.14971490.13792801295096

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