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Yorodumi- PDB-4jf8: Crystal structure of a TrwG component of type IV secretion system... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jf8 | ||||||
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Title | Crystal structure of a TrwG component of type IV secretion system protein from Bartonella birtlesii | ||||||
Components | TrwG component of type IV secretion system | ||||||
Keywords | PROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / cat scratch fever / secretion / host specific adhesion | ||||||
Function / homology | Function and homology information protein secretion by the type IV secretion system / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Bartonella birtlesii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jf8.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jf8.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jf8_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 4jf8_full_validation.pdf.gz | 425.7 KB | Display | |
Data in XML | 4jf8_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4jf8_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/4jf8 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/4jf8 | HTTPS FTP |
-Related structure data
Related structure data | 4kz1C 4lsoC 4meiC 4nhfC 4o3vC 2bhmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20344.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella birtlesii (bacteria) / Gene: trwG / Production host: Escherichia coli (E. coli) / References: UniProt: D0AAZ5 | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: BabiA.18388.a.B2 PS01693 at 25.7 mg/mL against JCSG+ screen condition A3, 0.2 M citrate, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, unique puck ID vff2-9, crystal tracking ID ...Details: BabiA.18388.a.B2 PS01693 at 25.7 mg/mL against JCSG+ screen condition A3, 0.2 M citrate, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, unique puck ID vff2-9, crystal tracking ID 240866a3, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→50 Å / Num. all: 31634 / Num. obs: 31529 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 34.59 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bhm Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.555 / SU ML: 0.033 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 15.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→50 Å
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Refine LS restraints |
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