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Yorodumi- PDB-6x6m: Peptide-bound structure of Marinomonas primoryensis peptide-bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x6m | ||||||
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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: 1.9 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 | 6x6m.cif.gz | 348.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x6m.ent.gz | 250.5 KB | Display | PDB format |
PDBx/mmJSON format | 6x6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/6x6m ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x6m | HTTPS FTP |
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-Related structure data
Related structure data | 6x5vC 6x5wC 6x6qC 58kgS 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 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: 436.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-1PE / | #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: 1.54 Å3/Da / Density % sol: 20.14 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 4.6 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→57.42 Å / Num. obs: 48424 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.98 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 1.697 / Num. unique obs: 20688 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 58kg Resolution: 1.9→57.39 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.9194 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: 32.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→57.39 Å
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Refine LS restraints |
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LS refinement shell |
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