+Open data
-Basic information
Entry | Database: PDB / ID: 1v19 | ||||||
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Title | 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS | ||||||
Components | 2-KETO-3-DEOXYGLUCONATE KINASE | ||||||
Keywords | TRANSFERASE / 2-KETO-3-DEOXYGLUCONATE KINASE / 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: 2.3 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 | 1v19.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v19.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/1v19 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/1v19 | HTTPS FTP |
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-Related structure data
Related structure data | 1v1aC 1v1bC 1v1sC 1rkdS C: citing same article (ref.) 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: 33470.184 Da / Num. of mol.: 2 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-DIO / | #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: 2.61 Å3/Da / Density % sol: 53 % / Description: CRYSTAL IS TWINNED |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.7 Details: MICROBATCH METHOD AT 291 K. 22.8 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 44% MPD, 10% DIOXANE AND 0.1 M HEPES BUFFER PH 7.7. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1.04 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 32439 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 9.1 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RKD Resolution: 2.3→44.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 444263.74 / 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 0.244
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.301 Å2 / ksol: 0.351572 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→44.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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