[English] 日本語
Yorodumi- PDB-4lso: Crystal structure of the soluble domain of a Type IV secretion sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lso | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the soluble domain of a Type IV secretion system protein VirB8 from Bartonella quintana Toulouse | ||||||
Components | Type IV secretion system protein virB8 | ||||||
Keywords | PROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dimer-monomer analysis / type IV secretion system / innate response / human pathogen / host specific protein / cell adhesion | ||||||
Function / homology | Function and homology information protein secretion by the type IV secretion system / : / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Bartonella quintana (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: MBio / Year: 2015 Title: Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems. Authors: Gillespie, J.J. / Phan, I.Q. / Scheib, H. / Subramanian, S. / Edwards, T.E. / Lehman, S.S. / Piitulainen, H. / Rahman, M.S. / Rennoll-Bankert, K.E. / Staker, B.L. / Taira, S. / Stacy, R. / ...Authors: Gillespie, J.J. / Phan, I.Q. / Scheib, H. / Subramanian, S. / Edwards, T.E. / Lehman, S.S. / Piitulainen, H. / Rahman, M.S. / Rennoll-Bankert, K.E. / Staker, B.L. / Taira, S. / Stacy, R. / Myler, P.J. / Azad, A.F. / Pulliainen, A.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lso.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lso.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lso_validation.pdf.gz | 418.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lso_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 4lso_validation.xml.gz | 9 KB | Display | |
Data in CIF | 4lso_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4lso ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4lso | HTTPS FTP |
-Related structure data
Related structure data | 4jf8C 4kz1SC 4meiC 4nhfC 4o3vC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20890.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: JK 31 / Gene: BQ10590, virB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FYW3 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.56 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: BaquA.18388.b.B2.PS01732 at 21 mg/mL against JCSG+ screen condition B9, 0.1 M Na citrate pH 5.0, 20% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242024b9, ...Details: BaquA.18388.b.B2.PS01732 at 21 mg/mL against JCSG+ screen condition B9, 0.1 M Na citrate pH 5.0, 20% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242024b9, unique puck ID fez5-10, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. all: 18788 / Num. obs: 18752 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 34.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4kz1 Resolution: 1.7→43.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.333 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.352 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|