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- PDB-4qih: The structure of mycobacterial glucosyl-3-phosphoglycerate phosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qih | ||||||
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Title | The structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c complexes with VO3 | ||||||
![]() | Glucosyl-3-phosphoglycerate phosphatase | ||||||
![]() | HYDROLASE / glycosyl-3-phosphoglycerate / glycolysis | ||||||
Function / homology | ![]() glucosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, W.H. / Zheng, Q.Q. / Jiang, D.Q. / Zhang, W. / Zhang, Q.Q. / Jin, J. / Li, X. / Yang, H.T. / Shaw, N. / Rao, Z. | ||||||
![]() | ![]() Title: Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a histidine phosphatase Authors: Zheng, Q. / Jiang, D. / Zhang, W. / Zhang, Q. / Zhao, Q. / Jin, J. / Li, X. / Yang, H. / Bartlam, M. / Shaw, N. / Zhou, W. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.1 KB | Display | ![]() |
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PDB format | ![]() | 127.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pz9SC ![]() 4pzaC 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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Unit cell |
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Components
#1: Protein | Mass: 24204.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WIC6, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, mannosyl-3-phosphoglycerate phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES sodium pH7.5, 10% 2-propanol, 20% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2013 Details: Double crystal Monochromator with Si (111) numerical link type. Mirror 1: colli mating, Rh-coated silicon single crystal, flat shaped. Mirror 2: focusing, Rh-co ated silicon single crystal, Toroidal.roidal. |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03935 Å / Relative weight: 1 |
Reflection | Resolution: 2.299→50 Å / Num. all: 23222 / Num. obs: 22409 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.055 / Rsym value: 0.05 / Net I/σ(I): 46 |
Reflection shell | Resolution: 2.299→2.34 Å / Redundancy: 7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 9 / Num. unique all: 1128 / Rsym value: 0.22 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PZ9 Resolution: 2.299→35.008 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 25.43 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.299→35.008 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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