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- PDB-1amx: COLLAGEN-BINDING DOMAIN FROM A STAPHYLOCOCCUS AUREUS ADHESIN -

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Basic information

Entry
Database: PDB / ID: 1amx
TitleCOLLAGEN-BINDING DOMAIN FROM A STAPHYLOCOCCUS AUREUS ADHESIN
ComponentsCOLLAGEN ADHESIN
KeywordsBACTERIAL ADHESIN / MSCRAMM
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 / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. ...Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / 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 / MIR / Resolution: 2 Å
AuthorsSymersky, J. / Narayana, S.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structure of the collagen-binding domain from a Staphylococcus aureus adhesin.
Authors: Symersky, J. / Patti, J.M. / Carson, M. / House-Pompeo, K. / Teale, M. / Moore, D. / Jin, L. / Schneider, A. / DeLucas, L.J. / Hook, M. / Narayana, S.V.
History
DepositionJun 19, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN ADHESIN


Theoretical massNumber of molelcules
Total (without water)20,3141
Polymers20,3141
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.000, 74.000, 56.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein COLLAGEN ADHESIN / CBD19


Mass: 20314.098 Da / Num. of mol.: 1 / Fragment: CBD (151 - 318)
Source method: isolated from a genetically manipulated source
Details: A 19-KDA FRAGMENT OF THE COLLAGEN-BINDING ADHESIN FROM A STAPHYLOCOCCUS AUREUS (HIS-TAG + RESIDUES 151-318)
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CNA / Plasmid: PQE504 / Cellular location (production host): CYTOPLASM / Gene (production host): CNA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: Q53654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.9 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 %PEG40001reservoir
250 mMHEPES1reservoir
32-3 %detergent n-octyl-beta-D-glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 12250 / % possible obs: 98.3 % / Observed criterion σ(I): -2 / Redundancy: 8.4 % / Rsym value: 0.078 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.125 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.308 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 102943 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 89.7 % / Rmerge(I) obs: 0.308

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
X-GEN(MSI)data reduction
X-GEN(MSI)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: AS IN X-PLOR 3.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -5 %RANDOM
Rwork0.2 ---
obs0.2 11232 91.3 %-
Displacement parametersBiso mean: 22.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 124 1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.366 -4 %
Rwork0.276 991 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.WATTOPOL.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor obs: 0.276

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