[English] 日本語
Yorodumi- PDB-4am9: CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4am9 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION CHAPERONE SYCD IN COMPLEX WITH A PEPTIDE OF THE TRANSLOCATOR YOPD | ||||||
Components |
| ||||||
Keywords | CHAPERONE / CHAPERONE BINDING DOMAIN / CHAPERONE PEPTIDE COMPLEX / PATHOGENICTIY FACTOR / TRANSLOCATOR / TETRATRICOPEPTIDE REPEAT / TPR / T3SS / VIRULENCE FACTOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Schreiner, M. / Niemann, H.H. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2012 Title: Crystal Structure of the Yersinia Enterocolitica Type III Secretion Chaperone Sycd in Complex with a Peptide of the Minor Translocator Yopd Authors: Schreiner, M. / Niemann, H.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4am9.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4am9.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 4am9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4am9_validation.pdf.gz | 460.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4am9_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 4am9_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 4am9_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4am9 ftp://data.pdbj.org/pub/pdb/validation_reports/am/4am9 | HTTPS FTP |
-Related structure data
Related structure data | 2vgyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16492.762 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703 Description: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703 Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: O87496 | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1165.358 Da / Num. of mol.: 1 / Fragment: RESIDUES 56-65 / Source method: obtained synthetically / Source: (synth.) YERSINIA ENTEROCOLITICA (bacteria) / References: UniProt: Q9R2G2, UniProt: P37132*PLUS | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | ChemComp-BU3 / ( #5: Water | ChemComp-HOH / | Sequence details | FIVE ADDITIONAL N-TERMINAL RESIDUES DUE TO PRESCISSION PROTEASE CLEAVAGE SYNTHETIC PEPTIDE (CHAIN B) ...FIVE ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.5 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 ...Details: RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 FOLD MOLAR EXCESS OF PEPTIDE OVER PROTEIN. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 11931 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 69.59 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 97 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VGY Resolution: 2.5→23.676 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML Details: RESIDUES 21-28 AND 160-163 FROM CHAIN A ARE DISORDERED, RESIDUES 65 FROM CHAIN B IS DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.501 Å2 / ksol: 0.301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→23.676 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|