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- PDB-2r6q: Crystal Structure of BclA-island Construct -

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Basic information

Entry
Database: PDB / ID: 2r6q
TitleCrystal Structure of BclA-island Construct
ComponentsBclA protein
KeywordsSTRUCTURAL PROTEIN / Bacillus anthracis exosporium / antigen / collagen-like glycoprotein
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / regulation of phagocytosis / extracellular matrix organization / extracellular matrix / 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 / molecular replacement / Resolution: 1.43 Å
AuthorsHan, B.W. / Herrin, B.R. / Turnbough Jr., C.L. / Cooper, M.D. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal structure of BclA-island Construct
Authors: Han, B.W. / Herrin, B.R. / Morris, G.M. / Choe, J. / Cooper, M.D. / Wilson, I.A.
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BclA protein


Theoretical massNumber of molelcules
Total (without water)13,6441
Polymers13,6441
Non-polymers00
Water3,027168
1
A: BclA protein

A: BclA protein

A: BclA protein


Theoretical massNumber of molelcules
Total (without water)40,9313
Polymers40,9313
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 area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.496, 67.496, 163.933
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, x-y, z+(0 -1 0) and -x+y, -x, z+(1 0 0).

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Components

#1: Protein BclA protein / Putative uncharacterized protein


Mass: 13643.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: bclA / Plasmid: pET15b / 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.: 168 / 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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: di-Sodium tartrate, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MarUSA MarMosaic -325 / Detector: CCD / Date: Mar 15, 2007
RadiationMonochromator: SINGLE CRYSTAL Si(111) BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 41307 / % possible obs: 98.9 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.035 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.43-1.4810.40.42837221.14691.6
1.48-1.5415.60.38840401.06698.6
1.54-1.6119.70.3240880.94499.8
1.61-1.721.40.23840881.097100
1.7-1.821.50.16441071.09100
1.8-1.9421.40.10241321.03100
1.94-2.1421.30.06641630.98399.9
2.14-2.4521.20.05141980.978100
2.45-3.0820.80.04442700.974100
3.08-5019.70.0344991.1198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.75 Å
Translation2.5 Å33.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BclA(PDB ID: 1WCK)

1wck


Resolution: 1.43→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.22 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.147 2086 5.1 %RANDOM
Rwork0.13 ---
obs0.13 41256 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.43→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 168 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221046
X-RAY DIFFRACTIONr_bond_other_d0.0010.02646
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9941452
X-RAY DIFFRACTIONr_angle_other_deg0.9631640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63427.30826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.77315164
X-RAY DIFFRACTIONr_chiral_restr0.1110.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021196
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02176
X-RAY DIFFRACTIONr_nbd_refined0.1820.2133
X-RAY DIFFRACTIONr_nbd_other0.1960.2625
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2543
X-RAY DIFFRACTIONr_nbtor_other0.0930.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1220.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.216
X-RAY DIFFRACTIONr_mcbond_it2.852956
X-RAY DIFFRACTIONr_mcbond_other1.4582300
X-RAY DIFFRACTIONr_mcangle_it3.5641186
X-RAY DIFFRACTIONr_scbond_it4.5866369
X-RAY DIFFRACTIONr_scangle_it5.6138258
X-RAY DIFFRACTIONr_rigid_bond_restr2.81232065
X-RAY DIFFRACTIONr_sphericity_free10.5283168
X-RAY DIFFRACTIONr_sphericity_bonded5.70531667
LS refinement shellResolution: 1.43→1.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 140 -
Rwork0.215 2546 -
all-2686 -
obs--89.03 %

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