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Open data
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Basic information
Entry | Database: PDB / ID: 5xhh | ||||||
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Title | crystal structure of Hcp1 from Salmonella typhimurium | ||||||
![]() | Hcp1 family type VI secretion system effector | ||||||
![]() | UNKNOWN FUNCTION / effector protein | ||||||
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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, Q.P. / Gao, Z.Q. / Zhang, H. / Dong, Y.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: crystal structure of Hcp1 from Salmonella typhimurium Authors: Lin, Q.P. / Gao, Z.Q. / Zhang, H. / Dong, Y.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
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Full document | ![]() | 441.2 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y12S ![]() 5wwy S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17753.834 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: sciK, BKC11_01420, BKC12_01390, BLM41_12425, DD95_17690, SEETMRM10961_1345 Plasmid: pET28a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 2.2 M Ammonium sulfate, 0.1M ammonium acetate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 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: 2.1→50 Å / Num. obs: 28203 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1432 / Rpim(I) all: 0.196 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Y12 Resolution: 2.1→41.386 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.386 Å
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Refine LS restraints |
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LS refinement shell |
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