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Yorodumi- PDB-3h49: Crystal structure of a putative Ribokinase (Apo Form) from E.coli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h49 | ||||||
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Title | Crystal structure of a putative Ribokinase (Apo Form) from E.coli at 1.8A resolution | ||||||
Components | Ribokinase | ||||||
Keywords | TRANSFERASE / Ribokinase / pfkB family / Sugar kinase ydjH / NYSGXRC / 11206A / PSI2 / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / Kinase | ||||||
Function / homology | Function and homology information carbohydrate kinase activity / D-galacturonate catabolic process / 2-dehydro-3-deoxygluconokinase activity / D-glucuronate catabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / DNA damage response / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative Ribokinase (Apo Form) from E.coli at 1.8A resolution. Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h49.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h49.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 3h49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/3h49 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/3h49 | HTTPS FTP |
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-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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35699.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TOP10 (Invitrogen) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b1772, JW5289, ydjH / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL References: UniProt: P77493, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: 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: 2.03 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M Ammonium Acetate,30% PEG 4K,Sodium Citrate 5.6pH, 10%Isopropanol., 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 315r / Detector: CCD / Date: Apr 8, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 51641 / Num. obs: 51641 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 7.7 / Num. unique all: 5073 / Rsym value: 0.48 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→34.71 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The main chain oxygen of Ser141 shows anisotropic effect.
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Displacement parameters | Biso mean: 17.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→34.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016
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