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- PDB-5yob: Crystal Structure of flavodoxin without engineered disulfide bond -

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Basic information

Entry
Database: PDB / ID: 5yob
TitleCrystal Structure of flavodoxin without engineered disulfide bond
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / fusion partner / FMN-binding protein / oxidation
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 ...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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.142 Å
AuthorsPu, M. / Xu, Z. / Song, G. / Liu, Z.J.
CitationJournal: Protein Cell / Year: 2018
Title: Protein crystal quality oriented disulfide bond engineering.
Authors: Pu, M. / Xu, Z. / Peng, Y. / Hou, Y. / Liu, D. / Wang, Y. / Liu, H. / Song, G. / Liu, Z.J.
History
DepositionOct 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)16,4294
Polymers15,7881
Non-polymers6413
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area7100 Å2
Unit cell
Length a, b, c (Å)32.232, 56.246, 41.058
Angle α, β, γ (deg.)90.00, 100.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flavodoxin


Mass: 15788.223 Da / Num. of mol.: 1 / Mutation: Y98W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: DVU_2680 / Production host: Escherichia coli (E. coli) / References: UniProt: P00323
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCL 0.1M Ammonium Sulfate 3.2M / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.142→31.656 Å / Num. obs: 38709 / % possible obs: 75 % / Redundancy: 4.4 % / Net I/σ(I): 32.21

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155-000refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8Q

1j8q


Resolution: 1.142→31.656 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 2000 5.17 %
Rwork0.1663 --
obs0.1668 38708 74.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.142→31.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 12 246 1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091203
X-RAY DIFFRACTIONf_angle_d1.0881640
X-RAY DIFFRACTIONf_dihedral_angle_d23.464413
X-RAY DIFFRACTIONf_chiral_restr0.087177
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1419-1.17050.369750.3352105X-RAY DIFFRACTION3
1.1705-1.20210.336280.3115495X-RAY DIFFRACTION14
1.2021-1.23750.3409580.2971054X-RAY DIFFRACTION30
1.2375-1.27740.2911930.27021728X-RAY DIFFRACTION49
1.2774-1.32310.24611280.23612352X-RAY DIFFRACTION67
1.3231-1.37610.25541620.22642975X-RAY DIFFRACTION84
1.3761-1.43870.21311890.20433443X-RAY DIFFRACTION98
1.4387-1.51460.21341910.17933518X-RAY DIFFRACTION99
1.5146-1.60940.1841910.16793512X-RAY DIFFRACTION100
1.6094-1.73370.20411910.15953508X-RAY DIFFRACTION100
1.7337-1.90820.191930.16353544X-RAY DIFFRACTION99
1.9082-2.18420.19131900.15633492X-RAY DIFFRACTION99
2.1842-2.75160.1641910.16463490X-RAY DIFFRACTION98
2.7516-31.66850.14221900.14993492X-RAY DIFFRACTION97

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