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Yorodumi- PDB-1v1b: 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v1b | ||||||
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Title | 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP | ||||||
Components | 2-KETO-3-DEOXYGLUCONATE KINASE | ||||||
Keywords | TRANSFERASE / 2-KETO-3-DEOXYGLUCONATE KINASE / ATP / THERMUS THERMOPHILUS / STRUCTURAL GENOMICS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI | ||||||
Function / homology | Function and homology information 2-dehydro-3-deoxygluconokinase / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / ATP binding Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tahirov, T.H. / Inagaki, E. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2004 Title: Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate. Authors: Ohshima, N. / Inagaki, E. / Yasuike, K. / Takio, K. / Tahirov, T.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and Preliminary Crystallographic Analysis of 2-Keto-3-Deoxygluconate Kinase from Thermus Thermophilus Authors: Inagaki, E. / Ukita, Y. / Kumei, M. / Kajihara, Y. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v1b.cif.gz | 237.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v1b.ent.gz | 193 KB | Display | PDB format |
PDBx/mmJSON format | 1v1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/1v1b ftp://data.pdbj.org/pub/pdb/validation_reports/v1/1v1b | HTTPS FTP |
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-Related structure data
Related structure data | 1v19SC 1v1aC 1v1sC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33470.184 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53W83*PLUS #2: Chemical | ChemComp-ATP / #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: 2.54 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM ATP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH ...Details: VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM ATP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND ATP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 |
Detector | Type: RIGAKU IMAGE PLATE R-AXISV / Detector: IMAGE PLATE / Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 36923 / % possible obs: 91.7 % / Observed criterion σ(I): -0.4 / Redundancy: 2.41 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.93 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 1.78 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V19 Resolution: 2.6→29.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 438892.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: CRYSTAL IS WITH HEMIHEDRAL TWINNING, TWINNING OPERATOR IS "H, -H-K, -L", TWINNING FRACTION IS 0.5
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3762 Å2 / ksol: 0.346608 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 300 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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