+Open data
-Basic information
Entry | Database: PDB / ID: 1amx | ||||||
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Title | COLLAGEN-BINDING DOMAIN FROM A STAPHYLOCOCCUS AUREUS ADHESIN | ||||||
Components | COLLAGEN ADHESIN | ||||||
Keywords | BACTERIAL ADHESIN / MSCRAMM | ||||||
Function / homology | Function and homology information collagen binding / peptidoglycan-based cell wall / cell adhesion / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Symersky, J. / Narayana, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1amx.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1amx.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1amx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/1amx ftp://data.pdbj.org/pub/pdb/validation_reports/am/1amx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.276 |