[English] 日本語
![](img/lk-miru.gif)
- PDB-1v1s: 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS (CRYSTAL... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1v1s | ||||||
---|---|---|---|---|---|---|---|
Title | 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS (CRYSTAL FORM 2) | ||||||
![]() | 2-KETO-3-DEOXYGLUCONATE KINASE | ||||||
![]() | TRANSFERASE / 2-KETO-3-DEOXYGLUCONATE KINASE / THERMUS THERMOPHILUS / STRUCTURAL GENOMICS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI | ||||||
Function / homology | ![]() 2-dehydro-3-deoxygluconokinase / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Inagaki, E. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 295 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 236 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 533.6 KB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 88.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v19SC ![]() 1v1aC ![]() 1v1bC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33470.184 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.2 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 28% V/V MPD, 10 MM CALCIUM CHLORIDE AND 0.1 M TRISODIUM CITRATE BUFFER, PH 5.6. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 27126 / % possible obs: 92.9 % / Observed criterion σ(I): -1 / Redundancy: 3.43 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.46 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2 / % possible all: 82 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V19 Resolution: 3.2→29.4 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 118387.2 / 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.7918 Å2 / ksol: 0.235014 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→29.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAIN / Rms dev position: 0 Å / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |