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- PDB-3tyj: Bacillus collagen-like protein of anthracis P159S mutant -

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Basic information

Entry
Database: PDB / ID: 3tyj
TitleBacillus collagen-like protein of anthracis P159S mutant
ComponentsBclA protein
KeywordsPROTEIN BINDING / exosporium
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / regulation of phagocytosis / extracellular matrix organization / extracellular space
Similarity search - Function
BclA, C-terminal domain / BclA C-terminal domain / Leader peptide, exosporium / : / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough Jr., C.L. / Cooper, M.D. / Wilson, I.A.
CitationJournal: Structure / Year: 2012
Title: Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores.
Authors: Kirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough, C.L. / Cooper, M.D. / Wilson, I.A.
History
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BclA protein


Theoretical massNumber of molelcules
Total (without water)15,6771
Polymers15,6771
Non-polymers00
Water1,910106
1
A: BclA protein

A: BclA protein

A: BclA protein


Theoretical massNumber of molelcules
Total (without water)47,0303
Polymers47,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6040 Å2
ΔGint-37 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.152, 68.152, 163.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: Protein BclA protein / Spore surface glycoprotein BclA


Mass: 15676.677 Da / Num. of mol.: 1 / Fragment: BclA-CTD / Mutation: P159S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BA_1222, bclA, GBAA_1222 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81JD7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.02
Details: 0.7M ammonium phosphate monobasic, 100mM sodium citrate, pH 5.02, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2010
RadiationMonochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 12588 / Num. obs: 12588 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.168 / Net I/σ(I): 11.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 617 / Rsym value: 0.647 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRrphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R6Q

2r6q


Resolution: 2.15→34.08 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23395 619 4.9 %RANDOM
Rwork0.20744 ---
obs0.20865 11957 96.91 %-
all-11957 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 0 106 1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022982
X-RAY DIFFRACTIONr_bond_other_d00.02596
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9881353
X-RAY DIFFRACTIONr_angle_other_deg4.57431504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85727.225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.22115150
X-RAY DIFFRACTIONr_chiral_restr0.0610.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211106
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02166
X-RAY DIFFRACTIONr_mcbond_it0.7651.5680
X-RAY DIFFRACTIONr_mcbond_other01.5287
X-RAY DIFFRACTIONr_mcangle_it1.40521108
X-RAY DIFFRACTIONr_scbond_it1.7273302
X-RAY DIFFRACTIONr_scangle_it3.1224.5241
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 40 -
Rwork0.25 840 -
obs--95.65 %

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