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Yorodumi- PDB-6x5w: Peptide-bound structure of Marinomonas primoryensis peptide-bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x5w | ||||||
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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: 1.8 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 | 6x5w.cif.gz | 360 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x5w.ent.gz | 258.4 KB | Display | PDB format |
PDBx/mmJSON format | 6x5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x5w_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 6x5w_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 6x5w_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 6x5w_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/6x5w ftp://data.pdbj.org/pub/pdb/validation_reports/x5/6x5w | HTTPS FTP |
-Related structure data
Related structure data | 6x5vC 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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: 525.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 543 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-1PE / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.45 Å3/Da / Density % sol: 56.78 % |
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Crystal grow | Temperature: 293 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: 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: 1.8→55.54 Å / Num. obs: 138852 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 16.22 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.809 / Num. unique obs: 51767 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5k8g Resolution: 1.8→55.54 Å / SU ML: 0.2103 / Cross valid method: FREE R-VALUE / σ(F): 2.24 / Phase error: 23.6832 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: 30.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→55.54 Å
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Refine LS restraints |
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LS refinement shell |
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