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Yorodumi- PDB-3t61: Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t61 | ||||||
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Title | Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021 | ||||||
Components | Gluconokinase | ||||||
Keywords | TRANSFERASE / PSI-BIOLOGY / Structural Genomics / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / Alpha/Beta / gluconokinase / Kinase / Gluconic acid | ||||||
Function / homology | Function and homology information gluconokinase / gluconokinase activity / carbohydrate metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021 Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t61.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t61.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3t61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t61_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 3t61_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 3t61_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 3t61_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t61 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t61 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Dimer |
-Components
#1: Protein | Mass: 22654.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: gntK, RB0698, SM_b21119 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: Q92VK3, gluconokinase #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: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2M Ammonium Phosphate Monobasic, 0.1 M Tris, 2% sucrose, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2011 / Details: mirrors |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 27740 / Num. obs: 27740 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2284 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→44.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 169839.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Extra density near the phosphate ion is not modeled.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.2911 Å2 / ksol: 0.343718 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→44.68 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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