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- PDB-3k5w: Crystal structure of a Carbohydrate kinase (YjeF family)from Heli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k5w | ||||||
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Title | Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori | ||||||
![]() | Carbohydrate kinase | ||||||
![]() | TRANSFERASE / KINASE / SAD / PFKB FAMILY / Carbohydrate kinase / 11206b / Helicobacter pylori / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | ![]() NAD(P)H-hydrate epimerase / metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NADHX epimerase activity / NADPHX epimerase activity / nicotinamide nucleotide metabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Satyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.9 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.2 KB | Display | ![]() |
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Full document | ![]() | 462.1 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52414.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TOP10 (Invitrogen) / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT THE REFERENCE TO UNP P56176 IS CORRECT AND THE DIFFERENCES ARE DUE TO NATURAL ...AUTHORS STATE THAT THE REFERENCE TO UNP P56176 IS CORRECT AND THE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M KH2PO4, 0.2M Ammonium Citrate pH 7.0 8% Acetonitrile 15% PEG 3,350., VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 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: 2.32→50 Å / Num. obs: 25967 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.1 % / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.089 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 27.9 % / Mean I/σ(I) obs: 7.8 / Rsym value: 0.65 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Authors state that the number of reflections are correct. Authors have used anomalous pairs as independent reflections in refinement.
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Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→48.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026
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