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- PDB-7r5i: High resolution Crystal structure of ExsFA, a Bacillus cereus spo... -

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Basic information

Entry
Database: PDB / ID: 7r5i
TitleHigh resolution Crystal structure of ExsFA, a Bacillus cereus spore exosporium protein
Components
  • Exosporium protein
  • GLN-GLU-ASP-PHE-SER-SER-ASP-SER-SER-PHE-SER
KeywordsSTRUCTURAL PROTEIN / ExsFA / BxpB / Bacillus cereus / exosporium / endospore
Function / homologymetal ion binding / Exosporium protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.08 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 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosporium protein
B: Exosporium protein
C: Exosporium protein
E: GLN-GLU-ASP-PHE-SER-SER-ASP-SER-SER-PHE-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3906
Polymers57,2584
Non-polymers1322
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.310, 82.587, 98.002
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 Exosporium protein / Exosporium protein ExsF


Mass: 18674.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: exsF, AT268_09550, COC69_11355, COK98_01700, COM79_21560, D0437_05965, FC702_13950, NCTC7464_04016
Production host: Escherichia coli (E. coli) / References: UniProt: Q7WTL3
#2: Protein/peptide GLN-GLU-ASP-PHE-SER-SER-ASP-SER-SER-PHE-SER


Mass: 1235.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.31 %
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: 0.85 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.08→63.15 Å / Num. obs: 200036 / % possible obs: 99.4 % / Redundancy: 42.4 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.009 / Rrim(I) all: 0.059 / Net I/σ(I): 25.5 / Num. measured all: 8490741 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.08-1.14315.178878540283570.7040.9225.2640.697.4
3.42-63.1540.20.03254686633510.0050.03142.392.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R1M

7r1m


Resolution: 1.08→63.15 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.188 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1597 9681 5 %RANDOM
Rwork0.1438 ---
obs0.1447 185693 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 198.81 Å2 / Biso mean: 23.988 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-0 Å2
2---0.59 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.08→63.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 13 449 3744
Biso mean--29.31 36.61 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0133644
X-RAY DIFFRACTIONr_bond_other_d0.0230.0143544
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.6355041
X-RAY DIFFRACTIONr_angle_other_deg1.6181.5648162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3865495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77121.401157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08715532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0971524
X-RAY DIFFRACTIONr_chiral_restr0.1290.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024254
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02810
X-RAY DIFFRACTIONr_rigid_bond_restr15.77937188
LS refinement shellResolution: 1.082→1.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.57 475 -
Rwork0.565 9262 -
all-9737 -
obs--66.04 %

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