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Yorodumi- PDB-4a0e: Crystal structure of the cytoplasmic N-terminal domain of Yersini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a0e | ||||||
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Title | Crystal structure of the cytoplasmic N-terminal domain of Yersinia pestis YscD | ||||||
Components | TYPE III SECRETION PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / SAD PHASING / TYPE III SECRETION SYSTEM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | YERSINIA PESTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.042 Å | ||||||
Authors | Lountos, G.T. / Tropea, J.E. / Waugh, D.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure of the Cytoplasmic Domain of Yersinia Pestis Yscd, an Essential Component of the Type III Secretion System Authors: Lountos, G.T. / Tropea, J.E. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a0e.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a0e.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a0e_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 4a0e_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 4a0e_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 4a0e_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a0e ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0e | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13483.413 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 2-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PJT173 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q1BZW5, UniProt: Q56975*PLUS #2: Water | ChemComp-HOH / | Sequence details | FIRST THREE GLYCINES ARE NON-NATIVE RESIDUES REMAINING AFTER TAG CLEAVAGE | |
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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: 2.56 Å3/Da / Density % sol: 51.9 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.085M TRIS HCL PH 8.5, 25.5% (W/V) PEG 4000, 0.17M NA ACETATE, 15% (V/V) GLYCEROL, 10 MM TCEP HYDROCHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Jun 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 18490 / % possible obs: 98.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5.1 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 2.04→2.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.042→39.409 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 23.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.686 Å2 / ksol: 0.352 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.042→39.409 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.8948 Å / Origin y: -14.1843 Å / Origin z: -46.6411 Å
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Refinement TLS group | Selection details: ALL |