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- PDB-5j6q: Cwp8 from Clostridium difficile -

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Basic information

Entry
Database: PDB / ID: 5j6q
TitleCwp8 from Clostridium difficile
ComponentsCell wall binding protein cwp8
KeywordsCELL ADHESION / cell wall protein / S-layer / CWB2 domain / toprim fold
Function / homology: / : / Cell wall binding protein Cwp8 domain 2 / Cell wall binding protein Cwp8 domain 3 / : / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / Cell wall binding protein cwp8
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRenko, M. / Usenik, A. / Turk, D.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0048 Slovenia
Ministry of Science and TechnologyOP13.1.1.2.02.0005 Slovenia
CitationJournal: Structure / Year: 2017
Title: The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6.
Authors: Usenik, A. / Renko, M. / Mihelic, M. / Lindic, N. / Borisek, J. / Perdih, A. / Pretnar, G. / Muller, U. / Turk, D.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Data collection / Database references
Revision 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall binding protein cwp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,62110
Polymers64,8171
Non-polymers8049
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-100 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.454, 63.432, 86.407
Angle α, β, γ (deg.)97.250, 100.530, 91.960
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cell wall binding protein cwp8


Mass: 64816.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: genomic DNA from C. difficile 630
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Gene: cwp8, CD630_27990 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q183N4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.7367rod-like
23.7367rod-like
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop2.04 M Ammonium sulfate 0.17 M Potassium acetate
2932vapor diffusion, sitting drop2.04 M Ammonium sulfate 0.17 M Potassium acetate 5 mM platinum potassium thiocyanate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.111
SYNCHROTRONESRF BM1421.069
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDSep 11, 2012
MARMOSAIC 225 mm CCD2CCDDec 10, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0691
Reflection

Entry-ID: 5J6Q / % possible obs: 95 %

Resolution (Å)Num. obsObserved criterion σ(I)Redundancy (%)Rmerge(I) obsRsym valueDiffraction-IDNet I/σ(I)
2.1-42.1522161.640.0630.054115.15
2.2-42921771.90.0940.084213.8
Reflection shell
Resolution (Å)Rmerge(I) obsRsym valueDiffraction-ID% possible all
2.1-2.1741.030.88169.45
0.921.562

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Processing

Software
NameClassification
XDSdata reduction
SHELXDEphasing
ARPmodel building
MAINrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→42.09 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9351 / Cross valid method: NONE / σ(F): 0 / Phase error: 27.2
Details: Free Kick ML target function uses all data for calculation of phase error estimates from randomly displaced atoms. Praznikar, J. & Turk, D. (2014) Free kick instead of cross-validation in ...Details: Free Kick ML target function uses all data for calculation of phase error estimates from randomly displaced atoms. Praznikar, J. & Turk, D. (2014) Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures. Acta Cryst. D70, 3124-3134.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 52186 100 %NONE
Rwork0.2291 ---
all0.2291 ---
obs0.2291 52186 95 %-
Solvent computationVDW probe radii: 1.6 Å / Bsol: 28.69 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 199.2 Å2 / Biso mean: 74.43 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.754 Å20.452 Å2-0.552 Å2
2--0.63 Å20.364 Å2
3---0.124 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 41 412 5006
LS refinement shellResolution: 2.1→2.135 Å
RfactorNum. reflection% reflection
Rfree0.359 1766 100 %
Rwork0.3371 1766 -

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