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- PDB-7r1m: Crystal structure of ExsFA, a Bacillus cereus spore exosporium protein -

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Basic information

Entry
Database: PDB / ID: 7r1m
TitleCrystal structure of ExsFA, a Bacillus cereus spore exosporium protein
ComponentsExosporium protein
KeywordsSTRUCTURAL PROTEIN / ExsFA / BxpB / Bacillus cereus / exosporium / endospore
Function / homologymetal ion binding / : / Exosporium protein
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.64 Å
AuthorsBrear, P. / Schack, S. / Christie, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L015889/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of ExsFA, a Bacillus cereus spore exosporium protein"
Authors: Brear, P. / Schack, S. / Christie, G.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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: Exosporium protein
B: Exosporium protein
C: Exosporium protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,88120
Polymers56,0223
Non-polymers2,85817
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-129 kcal/mol
Surface area14940 Å2
Unit cell
Length a, b, c (Å)95.298, 95.298, 117.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Exosporium protein / Exosporium protein ExsF


Mass: 18674.137 Da / Num. of mol.: 3 / Mutation: C5S, C12S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria)
Gene: exsF, AT268_09550, COC69_11355, COK98_01700, COM79_21560, D0437_05965, FC702_13950, NCTC7464_04016
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7WTL3

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Non-polymers , 5 types, 321 molecules

#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 22.5% (v/v) PEGSH, 0.2 M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→67.39 Å / Num. obs: 66528 / % possible obs: 100 % / Redundancy: 86.7 % / Biso Wilson estimate: 29.51 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.199 / Net I/σ(I): 19.2 / Num. measured all: 5766918
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.64-1.6786.10.527836532331.99618.56499.1
4.45-67.4482.5107.730041936400.0080.073100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.64→67.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3279 4.9 %RANDOM
Rwork0.209 ---
obs0.2103 63159 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.65 Å2 / Biso mean: 39.245 Å2 / Biso min: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.64→67.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 30 306 3728
Biso mean--54.01 44.08 -
Num. residues----460
LS refinement shellResolution: 1.641→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 252 -
Rwork0.447 4535 -
all-4787 -
obs--99.23 %

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