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- PDB-4bga: Nucleotide-bound open form of a putative sugar kinase MK0840 from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bga | |||||||||
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Title | Nucleotide-bound open form of a putative sugar kinase MK0840 from Methanopyrus kandleri | |||||||||
![]() | PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES | |||||||||
![]() | TRANSFERASE / ASKHA SUPERFAMILY / PHOSPHOTRANSFER / PSEUDOMUREIN | |||||||||
Function / homology | ![]() amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / metallopeptidase activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schacherl, M. / Baumann, U. | |||||||||
![]() | ![]() Title: Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 from Methanopyrus Kandleri Authors: Schacherl, M. / Waltersperger, S.M. / Baumann, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.5 KB | Display | ![]() |
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PDB format | ![]() | 208.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bg8SC ![]() 4bg9C ![]() 4bgbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35059.656 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/BGC.gif)
#2: Polysaccharide | #4: Sugar | ChemComp-BGC / |
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-Non-polymers , 4 types, 237 molecules ![](data/chem/img/K.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K / #5: Chemical | ChemComp-ADP / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | SUCROSE (SUC): CRYOPROTECSequence details | TRUNCATED CONSTRUCT LACKING THE FIRST 36 AMINO ACIDS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.24 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: MIXED WITH 5 MM ADP, 10 MM MACL2, CRYSTALLIZED IN 0.2 M POTASSIUM SODIUM TARTRATE AND 20% PEG 3350, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2010 |
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→73.6 Å / Num. obs: 54893 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 7.6 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.95 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 7.69 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.98 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BG8 CHAIN A Resolution: 2.6→73.568 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 20.53 / Stereochemistry target values: ML Details: FIRST 36 AMINO ACIDS OF THE PROTEIN ARE MISSING.GSH OVERHANG FROM THROMBIN-DIGESTED 6X-HIS TAG.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→73.568 Å
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Refine LS restraints |
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LS refinement shell |
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