+Open data
-Basic information
Entry | Database: PDB / ID: 3eaa | ||||||
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Title | Structure of a type six secretion system protein | ||||||
Components | EvpC | ||||||
Keywords | UNKNOWN FUNCTION / EvpC / T6SS | ||||||
Function / homology | Hcp1-like / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / EvpC Function and homology information | ||||||
Biological species | Edwardsiella tarda (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.794 Å | ||||||
Authors | Jobichen, C. / Sivaraman, J. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Structural basis for the secretion of EvpC: a key type VI secretion system protein from Edwardsiella tarda Authors: Jobichen, C. / Chakraborty, S. / Li, M. / Zheng, J. / Joseph, L. / Mok, Y.K. / Leung, K.Y. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eaa.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eaa.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 3eaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/3eaa ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3eaa | HTTPS FTP |
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-Related structure data
Related structure data | 1y12S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 2 - 163 / Label seq-ID: 2 - 163
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-Components
#1: Protein | Mass: 18123.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Edwardsiella tarda (bacteria) / Plasmid: pETM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6EE19 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Ammonium sulphate, 0.1M BIS-TRIS(pH 6.5), 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 30, 2007 |
Radiation | Monochromator: CN1707 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.794→50 Å / Num. all: 9595 / Num. obs: 9073 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 33.95 Å2 / Rsym value: 0.163 / Net I/σ(I): 7.5 |
-Processing
Software |
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Refinement | Starting model: PDB code 1Y12 Resolution: 2.794→28.963 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 2.2 / Phase error: 27.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.433 Å2 / ksol: 0.226 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.79 Å2 / Biso mean: 27.644 Å2 / Biso min: 6.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.794→28.963 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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