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- PDB-2f68: Crystal structure of collagen adhesin (CNA) from S. aureus -

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Basic information

Entry
Database: PDB / ID: 2f68
TitleCrystal structure of collagen adhesin (CNA) from S. aureus
ComponentsCollagen adhesin
KeywordsCELL ADHESION / Beta barrel / domain swap
Function / homology
Function and homology information


collagen binding / peptidoglycan-based cell wall / cell adhesion / extracellular region
Similarity search - Function
Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily ...Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZong, Y. / Narayana, S.V.L.
CitationJournal: Embo J. / Year: 2005
Title: A 'Collagen Hug' model for Staphylococcus aureus CNA binding to collagen.
Authors: Zong, Y. / Xu, Y. / Liang, X. / Keene, D.R. / Hook, A. / Gurusiddappa, S. / Hook, M. / Narayana, S.V.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
X: Collagen adhesin


Theoretical massNumber of molelcules
Total (without water)34,3891
Polymers34,3891
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.982, 106.427, 44.083
Angle α, β, γ (deg.)90.00, 116.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Collagen adhesin


Mass: 34388.715 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cna / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q53654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 3.2 M Ammonium Sulfate, 0.1 M NaCl, 0.05 M Hepes, PH. 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 20, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→53 Å / Num. all: 29614 / Num. obs: 28383 / % possible obs: 95.83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 36
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 1.35 / Num. unique all: 2781 / Rsym value: 0.09 / % possible all: 70

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
REFMAC5.1.24refinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→52 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1957 8 %Random
Rwork0.195 ---
obs0.292 24460 96 %-
all-25502 --
Refinement stepCycle: LAST / Resolution: 1.95→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 0 166 2482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.734
X-RAY DIFFRACTIONc_bond_d0.005

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