+Open data
-Basic information
Entry | Database: PDB / ID: 5xeu | ||||||
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Title | crystal structure of Hcp2 from Salmonella typhimurium | ||||||
Components | Hcp1 family type VI secretion system effectorType VI secretion system | ||||||
Keywords | CYTOSOLIC PROTEIN / hexameric | ||||||
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 / Hcp1 family type VI secretion system effector Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lin, Q.P. / Gao, Z.Q. / Zhang, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Crystal structure of the putative cytoplasmic protein STM0279 (Hcp2) from Salmonella typhimurium Authors: Lin, Q.P. / Gao, Z.Q. / Geng, Z. / Zhang, H. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xeu.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xeu.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xeu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xeu ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xeu | 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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Unit cell |
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-Components
#1: Protein | Mass: 17749.885 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) Gene: sciM, BKC11_01435, BLM41_12410, DD95_17705, SEETMRM10961_1365 Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9L4J8 |
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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: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 2.2M Ammonium sulfate, 0.1M ammonium acetate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 21754 / % possible obs: 99.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.054 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1098 / Rpim(I) all: 0.395 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y12 Resolution: 3→32.799 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 47.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→32.799 Å
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Refine LS restraints |
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LS refinement shell |
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