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Open data
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Basic information
Entry | Database: PDB / ID: 2wgl | ||||||
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Title | Crystal structure of Helicobactor pylori UreF | ||||||
![]() | UREASE ACCESSORY PROTEIN UREF | ||||||
![]() | METAL BINDING PROTEIN / CYTOPLASM / VIRULENCE / CHAPERONE / NICKEL INSERTION | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fong, Y.H. / Chen, Y.W. / Wong, K.B. | ||||||
![]() | ![]() Title: Crystal Structure of H. Pylori Uref Authors: Fong, Y.H. / Chen, Y.W. / Wong, K.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139 KB | Display | ![]() |
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PDB format | ![]() | 117.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 29120.783 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.04 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.12 Å / Num. obs: 51513 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.241 / % possible all: 93.9 |
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Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2→35.26 Å / SU ML: 0.08 / σ(F): 0.08 / Phase error: 22.04 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.741 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→35.26 Å
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Refine LS restraints |
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LS refinement shell |
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