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Yorodumi- PDB-6x5v: Peptide-bound structure of Marinomonas primoryensis peptide-bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x5v | ||||||
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Title | Peptide-bound structure of Marinomonas primoryensis peptide-binding domain | ||||||
Components |
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Keywords | PROTEIN BINDING / peptide-binding domain / protein-binding domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Marinomonas primoryensis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Guo, S. / Davies, P.L. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Molecular basis for a bacterial adhesins peptide-binding module Authors: Davies, P.L. / Guo, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x5v.cif.gz | 327.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x5v.ent.gz | 256.4 KB | Display | PDB format |
PDBx/mmJSON format | 6x5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/6x5v ftp://data.pdbj.org/pub/pdb/validation_reports/x5/6x5v | HTTPS FTP |
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-Related structure data
Related structure data | 6x5wC 6x6mC 6x6qC 5k8gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52963.352 Da / Num. of mol.: 1 / Fragment: Peptide-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3 | ||||||
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#2: Protein/peptide | Mass: 426.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.81 % |
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Crystal grow | Temperature: 298 K / Method: microbatch Details: ~0.1 M calcium chloride, ~0.1 M sodium acetate (pH 4.6), ~30% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→52.5 Å / Num. obs: 138852 / % possible obs: 89 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.52 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 3829 / CC1/2: 0.724 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K8G Resolution: 1.6→52.48 Å / SU ML: 0.2078 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.2475 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→52.48 Å
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Refine LS restraints |
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LS refinement shell |
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