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- PDB-6fsi: Crystal structure of semiquinone Flavodoxin 1 from Bacillus cereu... -

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Basic information

Entry
Database: PDB / ID: 6fsi
TitleCrystal structure of semiquinone Flavodoxin 1 from Bacillus cereus (1.32 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
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 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 19, 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
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-15 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.906, 45.099, 82.030
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 (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Gene: BC_1376 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81G35
#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.: 182 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
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: 0.6983 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6983 Å / Relative weight: 1
ReflectionResolution: 1.32→35.15 Å / Num. obs: 34618 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 23.2
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 13.6 / Num. unique obs: 1678 / CC1/2: 0.989 / Rpim(I) all: 0.046 / Rrim(I) all: 0.102 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1wsb


Resolution: 1.32→29.459 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 9.96
RfactorNum. reflection% reflection
Rfree0.1262 1730 5.01 %
Rwork0.1046 --
obs0.1056 34557 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.37 Å2 / Biso mean: 9.7963 Å2 / Biso min: 1.63 Å2
Refinement stepCycle: final / Resolution: 1.32→29.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 48 187 1364
Biso mean--24.72 21.01 -
Num. residues----147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.32-1.35890.13261390.088526832822100
1.3589-1.40270.11931350.087627112846100
1.4027-1.45290.11271270.087227432870100
1.4529-1.5110.11391440.081426752819100
1.511-1.57980.0941520.081826832835100
1.5798-1.66310.11311390.084727392878100
1.6631-1.76730.11981400.092627162856100
1.7673-1.90370.12091480.094527142862100
1.9037-2.09520.121420.097427452887100
2.0952-2.39830.11571600.097227572917100
2.3983-3.02110.13471530.118627762929100
3.0211-29.4660.15211510.13492885303698

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