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- PDB-5xch: Crystal structure of Wild type Vps29 complexed with Zn+2 from Ent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xch | ||||||
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Title | Crystal structure of Wild type Vps29 complexed with Zn+2 from Entamoeba histolytica | ||||||
![]() | Vacuolar protein sorting-associated protein 29![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Srivastava, V.K. / Yadav, R. / Tomar, P. / Gourinath, S. / Datta, S. | ||||||
![]() | ![]() Title: Structural and thermodynamic characterization of metal binding in Vps29 from Entamoeba histolytica: implication in retromer function. Authors: Srivastava, V.K. / Yadav, R. / Watanabe, N. / Tomar, P. / Mukherjee, M. / Gourinath, S. / Nakada-Tsukui, K. / Nozaki, T. / Datta, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.3 KB | Display | ![]() |
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PDB format | ![]() | 61.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xceSC ![]() 5xcjC ![]() 5xckC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 21876.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HM-1:IMSS / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 % w/v PEG 20000, 20 % v/v PEGMME 550, 0.02 M of alcohol MIX, 0.1 M MES/Imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.45 |
Reflection | Resolution: 2.85→40.9 Å / Num. obs: 8561 / % possible obs: 98 % / Redundancy: 11.2 % / Net I/σ(I): 21 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5XCE Resolution: 2.85→40.9 Å / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 33.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→40.9 Å
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Refine LS restraints |
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LS refinement shell |
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