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- PDB-6k1t: The structure of Francisella virulence factor BioJ -

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Basic information

Entry
Database: PDB / ID: 6k1t
TitleThe structure of Francisella virulence factor BioJ
ComponentsAlpha/beta hydrolase fold family protein
KeywordsHYDROLASE / virulence factor BioJ
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase fold family protein
Function and homology information
Biological speciesFrancisella philomiragia subsp. philomiragia ATCC 25015 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.584 Å
AuthorsOuyang, S. / Guan, H. / Zhang, S.
CitationJournal: Iscience / Year: 2019
Title: Molecular Basis of BioJ, a Unique Gatekeeper in Bacterial Biotin Synthesis.
Authors: Wei, W. / Guan, H. / Zhu, T. / Zhang, S. / Fan, C. / Ouyang, S. / Feng, Y.
History
DepositionMay 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold family protein


Theoretical massNumber of molelcules
Total (without water)35,4791
Polymers35,4791
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12990 Å2
Unit cell
Length a, b, c (Å)43.943, 67.313, 55.571
Angle α, β, γ (deg.)90.00, 112.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha/beta hydrolase fold family protein


Mass: 35479.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella philomiragia subsp. philomiragia ATCC 25015 (bacteria)
Gene: BZ13_192 / Production host: Escherichia coli (E. coli) / References: UniProt: C6YW90
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 289.15 K / Method: counter-diffusion
Details: 20% (v/v) PEG 6000, 100mM BICINE/sodium hydroxide (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.58→51.32 Å / Num. obs: 37190 / % possible obs: 91.5 % / Redundancy: 3 % / Net I/σ(I): 6.7
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 5609

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
autoPROCdata collection
autoPROCdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.584→40.208 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.235 1808 4.89 %
Rwork0.2067 --
obs0.2082 37007 90.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.584→40.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 0 216 2659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062505
X-RAY DIFFRACTIONf_angle_d0.8083394
X-RAY DIFFRACTIONf_dihedral_angle_d2.7261503
X-RAY DIFFRACTIONf_chiral_restr0.051368
X-RAY DIFFRACTIONf_plane_restr0.005432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5838-1.62660.27411330.2592832X-RAY DIFFRACTION95
1.6266-1.67450.30071380.24752778X-RAY DIFFRACTION94
1.6745-1.72850.26281370.24272767X-RAY DIFFRACTION93
1.7285-1.79030.2731190.24582691X-RAY DIFFRACTION90
1.7903-1.8620.28581420.23982662X-RAY DIFFRACTION90
1.862-1.94680.3412880.26351742X-RAY DIFFRACTION85
1.9468-2.04940.26861210.21142770X-RAY DIFFRACTION93
2.0494-2.17780.23181500.20682811X-RAY DIFFRACTION94
2.1778-2.34590.26671310.19912854X-RAY DIFFRACTION96
2.3459-2.58190.2181720.20982839X-RAY DIFFRACTION96
2.5819-2.95550.22931630.20712924X-RAY DIFFRACTION98
2.9555-3.72320.21511580.19182832X-RAY DIFFRACTION95
3.7232-40.22050.20591560.1822697X-RAY DIFFRACTION89

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