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- PDB-1saz: Membership in the ASKHA Superfamily: Enzymological Properties and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1saz | ||||||
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Title | Membership in the ASKHA Superfamily: Enzymological Properties and Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima | ||||||
![]() | Probable butyrate kinase 2 | ||||||
![]() | TRANSFERASE / ASKHA (ACETATE AND SUGAR KINASES / HSC70 / ACTIN) SUPERFAMILY / BUTYRATE KINASE / ACETATE KINASE / ISOBUTYRATE KINASE / TWO SIMILAR DOMAINS / AMPPCP / BUTYRATE / ISOBUTYRATE / DISULFIDE BOND / ENZYME MECHANISM | ||||||
Function / homology | ![]() butyrate kinase / butyrate kinase activity / acetate kinase activity / acetate metabolic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Diao, J. / Cooper, D.R. / Sanders, D.A. / Hasson, M.S. | ||||||
![]() | ![]() Title: Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases. Authors: Diao, J. / Hasson, M.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization of Butyrate Kinase 2 from Thermotoga Maritima Mediated by Vapour Diffusion of Acetic Acid Authors: Diao, J.S. / Cooper, D.R. / Sanders, D.A. / Hasson, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 731.4 KB | Display | ![]() |
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Full document | ![]() | 740.7 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is an octamer generated from the monomer in the asymmetric unit by the operations: -X,-Y,Z; -Y,X,Z; Y,-X,Z; -X,Y,-Z; X,-Y,-Z; Y,X,-Z; and -Y,-X,-Z |
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Components
#1: Protein | Mass: 43474.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-ACP / | ||
#4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: n-octyl-beta-D-glucoside, Tris-HCl pH 8.5, NaCl, DTT, glycerol, ADP, MgCl2, isobutyrate, sodium formate, acetate. AMPPCP, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2002 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→98 Å / Num. obs: 17673 / % possible obs: 87.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 58 Å2 / Rsym value: 0.122 / Net I/σ(I): 15.9 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.67 / Num. unique all: 1296 / Rsym value: 0.567 / % possible all: 65.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 46.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→43.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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