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Yorodumi- PDB-4qih: The structure of mycobacterial glucosyl-3-phosphoglycerate phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qih | ||||||
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Title | The structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c complexes with VO3 | ||||||
Components | Glucosyl-3-phosphoglycerate phosphatase | ||||||
Keywords | HYDROLASE / glycosyl-3-phosphoglycerate / glycolysis | ||||||
Function / homology | Function and homology information glucosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qih.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qih.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qih_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 4qih_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 4qih_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4qih_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/4qih ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qih | HTTPS FTP |
-Related structure data
Related structure data | 4pz9SC 4pzaC S: Starting model for refinement C: citing same article (ref.) |
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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: 24204.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gpgP, MT2492, Rv2419c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.03935 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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