[English] 日本語
Yorodumi- PDB-2gmu: Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gmu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with PLP-glutamate ketimine intermediate | ||||||
Components | Putative pyridoxamine 5-phosphate-dependent dehydrase, WbdK | ||||||
Keywords | TRANSFERASE / colitose / deoxysugar / aspartate aminotransferase / PLP / o-antigen | ||||||
Function / homology | Function and homology information dTDP-4-amino-4,6-dideoxygalactose transaminase activity / Transferases; Transferring nitrogenous groups; Transaminases / polysaccharide biosynthetic process / pyridoxal phosphate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli O55:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Cook, P.D. / Thoden, J.B. / Holden, H.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme. Authors: Cook, P.D. / Thoden, J.B. / Holden, H.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gmu.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gmu.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gmu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2gmu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2gmu_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 2gmu_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/2gmu ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gmu | HTTPS FTP |
-Related structure data
Related structure data | 2gmsSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44352.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O55:H7 (bacteria) / Species: Escherichia coli / Strain: O55:H7, Strain 5a / Gene: wbdK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: GenBank: 18266409, UniProt: Q9F118*PLUS #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.44 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch / pH: 6 Details: 14% PEG 3400, 0.05 M MES, 0.2 M MgCl2, 0.1 M NaCl, 1 mM pyridoxal-5-phosphate, 2 mM glutamate, 2 mM GDP, pH 6.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 30, 2005 / Details: supper mirrors |
Radiation | Monochromator: ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 72854 / Num. obs: 72854 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.0546 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 7334 / Rsym value: 0.31 / % possible all: 79 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2GMS Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|