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- PDB-6bt4: Crystal structure of the SLH domain of Sap from Bacillus anthraci... -

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Basic information

Entry
Database: PDB / ID: 6bt4
TitleCrystal structure of the SLH domain of Sap from Bacillus anthracis in complex with a pyruvylated SCWP unit
ComponentsS-layer protein sap
KeywordsSTRUCTURAL PROTEIN / S-layer homology domain / Secondary cell wall polysaccharide / cell wall / anthrax / S-layer
Function / homology
Function and homology information


S-layer / extracellular region
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Chem-KPM / S-layer protein sap
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsSychantha, D. / Chapman, R.N. / Bamford, N.C. / Boons, G.J. / Howell, P.L. / Clarke, A.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)TGC 114045 Canada
Canadian Institutes of Health Research (CIHR)MOP 43998 Canada
CitationJournal: Biochemistry / Year: 2018
Title: Molecular Basis for the Attachment of S-Layer Proteins to the Cell Wall of Bacillus anthracis.
Authors: Sychantha, D. / Chapman, R.N. / Bamford, N.C. / Boons, G.J. / Howell, P.L. / Clarke, A.J.
History
DepositionDec 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: S-layer protein sap
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8694
Polymers22,1821
Non-polymers6873
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.560, 76.560, 97.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein S-layer protein sap / / Surface array protein / Surface layer protein


Mass: 22182.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli (E. coli) / References: UniProt: P49051
#2: Chemical ChemComp-KPM / 2-(acetylamino)-4-O-{2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranosyl}-2-deoxy-beta-D-glucopyranose


Mass: 494.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H30N2O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.22 Å3/Da / Density % sol: 61.76 % / Description: bipyrimidal
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9996 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9996 Å / Relative weight: 1
ReflectionResolution: 2.3→47.32 Å / Num. obs: 13241 / % possible obs: 99.41 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.05345 / Net I/σ(I): 21.29
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 6 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.95 / Num. unique obs: 1272 / % possible all: 97.92

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
Cootmodel building
PHENIXphasing
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PYW

3pyw


Resolution: 2.306→47.316 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.65
RfactorNum. reflection% reflection
Rfree0.2182 1326 10.02 %
Rwork0.1848 --
obs0.1881 13236 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.306→47.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 44 31 1336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081330
X-RAY DIFFRACTIONf_angle_d1.0951804
X-RAY DIFFRACTIONf_dihedral_angle_d13.528497
X-RAY DIFFRACTIONf_chiral_restr0.04205
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3063-2.39860.29171440.23151282X-RAY DIFFRACTION98
2.3986-2.50780.26011420.19511280X-RAY DIFFRACTION100
2.5078-2.640.23031470.19661321X-RAY DIFFRACTION100
2.64-2.80530.24741430.20421299X-RAY DIFFRACTION100
2.8053-3.02190.26371470.23191315X-RAY DIFFRACTION100
3.0219-3.3260.26311450.21641322X-RAY DIFFRACTION100
3.326-3.8070.20271480.16321320X-RAY DIFFRACTION100
3.807-4.79570.18131500.15271352X-RAY DIFFRACTION99
4.7957-47.32580.20461600.18581419X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7375-5.3554.98495.0664-4.86384.72650.0672-0.81741.38010.8491-0.1662-0.7656-0.5630.55460.26610.46170.03090.00950.6025-0.09290.52256.1674-9.5433-5.8486
29.12772.73992.36437.2245-0.83260.98990.4358-1.39730.38430.7197-0.27660.1197-0.04-0.1182-0.15270.490.01020.14370.63790.0110.3942-5.1374-16.2212-8.9443
34.04265.86521.03129.4289-0.4874.46890.9957-1.72161.05760.3556-1.25241.6686-0.4987-0.20270.10710.45230.02780.13550.7003-0.01370.9474-19.7234-9.2742-11.741
45.9028-1.02110.3687.60261.25334.5326-0.03220.27540.253-0.09920.09750.26960.1007-0.3525-0.07420.26470.00210.07060.35540.10310.3976-15.7707-20.562-15.522
56.4199-0.0278-2.76786.1162-0.06427.5032-0.1290.13670.0529-0.28680.13920.5353-0.0199-0.40710.00810.2936-0.0146-0.01150.34440.04260.2987-0.5097-14.0923-27.1873
62.0725-0.75350.3166.31722.36292.4367-0.2760.2275-0.5797-0.3687-0.09480.51030.3984-0.2810.39710.48750.02010.11130.4720.00330.52082.145-22.1421-29.6051
75.5135-1.8163-4.66029.70931.55843.9917-0.1797-0.4218-0.7308-0.5304-0.3663-0.72350.60980.84430.56270.41270.10320.02620.48710.03470.49716.4247-22.2333-20.8339
88.47592.6671-1.16744.0903-5.99619.93-0.0811-0.03020.1679-0.00120.18970.01180.17560.1215-0.14650.35390.03630.10040.35460.00240.35931.4246-9.7638-15.5742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 156 )
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 209 )

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