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- PDB-7xt1: Crystal structure of Bypass-of-forespore protein C from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 7xt1
TitleCrystal structure of Bypass-of-forespore protein C from Bacillus Subtilis
ComponentsProtein BofC
KeywordsSIGNALING PROTEIN / sporulation
Function / homologyBypass of forespore C, C-terminal / Bypass-of-forespore C, N-terminal / Bypass of forespore C, C-terminal domain superfamily / Bypass-of-forespore C, N-terminal domain superfamily / BofC C-terminal domain / Bypass of Forespore C, N terminal / sporulation resulting in formation of a cellular spore / Protein BofC
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.98 Å
AuthorsZhang, X.Y. / Jiang, L.G. / Huang, M.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82070142 China
CitationJournal: Catalysts / Year: 2022
Title: Structural Studies of Bypass of Forespore Protein C from Bacillus Subtilis to Reveal Its Inhibitory Molecular Mechanism for SpoIVB
Authors: Zhang, X. / Sun, G. / Yuan, C. / Jiang, L. / Huang, M.
History
DepositionMay 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 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: Protein BofC


Theoretical massNumber of molelcules
Total (without water)19,6621
Polymers19,6621
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.427, 46.004, 93.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein BofC / Bypass-of-forespore protein C


Mass: 19662.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: bofC, BSU27750
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O05391
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.82 Å3/Da / Density % sol: 32.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate trihydrate pH4.5, 30% w/v polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 10268 / % possible obs: 97.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 30.1
Reflection shellResolution: 1.98→2.07 Å / Rmerge(I) obs: 1.421 / Num. unique obs: 988 / CC1/2: 0.693 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.98→46.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.665 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 512 5 %RANDOM
Rwork0.2232 ---
obs0.2258 9716 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.76 Å2 / Biso mean: 48.871 Å2 / Biso min: 29.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.1 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.98→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 0 23 1130
Biso mean---55.08 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121135
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161027
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6331531
X-RAY DIFFRACTIONr_angle_other_deg0.5511.562404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6415135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.204104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90610204
X-RAY DIFFRACTIONr_chiral_restr0.0780.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
LS refinement shellResolution: 1.981→2.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 28 -
Rwork0.364 665 -
all-693 -
obs--91.67 %

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