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- PDB-6gv8: Characterization of extracellular matrix binding protein- (Embp)-... -

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Basic information

Entry
Database: PDB / ID: 6gv8
TitleCharacterization of extracellular matrix binding protein- (Embp)-mediated Staphylococcus epidermidis adherence to fibronectin
ComponentsHyperosmolarity resistance protein Emb
KeywordsCELL ADHESION / EMBP / Staphylococcus epidermidis / FG-repeat
Function / homology
Function and homology information


: / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Extracellular matrix-binding protein Ebh domain / Domain of unknown function DUF1542 / Domain of Unknown Function (DUF1542) / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Atypical Rib domain / Atypical Rib domain / FIVAR domain ...Extracellular matrix-binding protein Ebh domain / Domain of unknown function DUF1542 / Domain of Unknown Function (DUF1542) / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Atypical Rib domain / Atypical Rib domain / FIVAR domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide
Similarity search - Domain/homology
ECM-binding protein homolog / Extracellular matrix-binding protein ebh
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.394 Å
AuthorsBuettner, H. / Rohde, H. / Perbandt, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationEXC1074 Germany
CitationJournal: Mbio / Year: 2020
Title: A Giant Extracellular Matrix Binding Protein of Staphylococcus epidermidis Binds Surface-Immobilized Fibronectin via a Novel Mechanism.
Authors: Buttner, H. / Perbandt, M. / Kohler, T. / Kikhney, A. / Wolters, M. / Christner, M. / Heise, M. / Wilde, J. / Weisselberg, S. / Both, A. / Betzel, C. / Hammerschmidt, S. / Svergun, D. / ...Authors: Buttner, H. / Perbandt, M. / Kohler, T. / Kikhney, A. / Wolters, M. / Christner, M. / Heise, M. / Wilde, J. / Weisselberg, S. / Both, A. / Betzel, C. / Hammerschmidt, S. / Svergun, D. / Aepfelbacher, M. / Rohde, H.
History
DepositionJun 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Hyperosmolarity resistance protein Emb


Theoretical massNumber of molelcules
Total (without water)18,8371
Polymers18,8371
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.800, 34.250, 40.163
Angle α, β, γ (deg.)95.910, 103.110, 113.540
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hyperosmolarity resistance protein Emb


Mass: 18836.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: ebh, CTJ08_00575 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G7I4G8, UniProt: Q5HPA2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: Morpheus Screen E12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 91935 / % possible obs: 86.8 % / Redundancy: 3.7 % / Net I/σ(I): 18.95
Reflection shellResolution: 1.39→1.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.394→30.653 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.43
RfactorNum. reflection% reflection
Rfree0.1885 1214 4.9 %
Rwork0.1563 --
obs0.158 24798 86.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.69 Å2 / Biso mean: 15.4675 Å2 / Biso min: 4.67 Å2
Refinement stepCycle: final / Resolution: 1.394→30.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 0 262 1489
Biso mean---26.14 -
Num. residues----157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3942-1.45010.28841210.2322352247379
1.4501-1.51610.24781430.21012592273586
1.5161-1.5960.19361440.16752696284089
1.596-1.6960.21171180.16252569268784
1.696-1.82690.19321310.16762694282590
1.8269-2.01070.18981370.15662720285790
2.0107-2.30160.18271230.1452480260382
2.3016-2.89940.18691360.15342739287591
2.8994-30.66050.16651610.13952742290391

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