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Yorodumi- PDB-2r0t: Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r0t | ||||||
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Title | Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine | ||||||
Components | Pyridoxamine 5-phosphate-dependent dehydrase | ||||||
Keywords | TRANSFERASE / colitose / aspartate aminotransferase / geminal diamine / pyridoxal phosphate | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Cook, P.D. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation Authors: Cook, P.D. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r0t.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0t.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 2r0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r0t_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2r0t_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2r0t_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 2r0t_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0t ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0t | HTTPS FTP |
-Related structure data
Related structure data | 2gmuS S: Starting model for refinement |
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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: 44343.453 Da / Num. of mol.: 2 / Mutation: H188K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O55:H7 Strain 5a / Gene: wbdK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9F118 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | LYSINE 188 IS COVALENTLY | |
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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: 2.38 Å3/Da / Density % sol: 48.26 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 24% PEG 3400, 100mM MES, 600mM KCl, 2mM PLP, 2mM 2-oxoglutarate, pH 6.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: BRUKER PROTEUM / Detector: CCD / Date: Jun 20, 2007 / Details: montel opics |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 177105 / Num. obs: 60929 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.0626 / Net I/σ(I): 9.87 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.42 % / Mean I/σ(I) obs: 1.55 / Num. unique all: 7757 / Rsym value: 0.4 / % possible all: 83.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GMU Resolution: 1.9→30 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.852 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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