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Yorodumi- PDB-2var: Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxyglucon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2var | |||||||||
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Title | Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate | |||||||||
Components | FRUCTOKINASE | |||||||||
Keywords | TRANSFERASE / KINASE / SULFOLOBUS SOLFATARICUS / PFKB FAMILY CARBOHYDRATE KINASE / 2- KETO-3-DEOXYGLUCONATE KINASEKINASE / 2- KETO-3-DEOXYGLUCONATE KINASE | |||||||||
Function / homology | Function and homology information 2-dehydro-3-deoxyglucono/galactono-kinase / 2-dehydro-3-deoxygalactonokinase activity / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / ATP binding Similarity search - Function | |||||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Potter, J.A. / Theodossis, A. / Kerou, M. / Lamble, H.J. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: The Structure of Sulfolobus Solfataricus 2-Keto-3-Deoxygluconate Kinase. Authors: Potter, J.A. / Kerou, M. / Lamble, H.J. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2var.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2var.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 2var.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2var ftp://data.pdbj.org/pub/pdb/validation_reports/va/2var | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 34918.715 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97U29, fructokinase #3: Sugar | |
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-Non-polymers , 4 types, 466 molecules
#2: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.84 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→90.5 Å / Num. obs: 80339 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 99.5 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→61.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.825 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 23.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→61.66 Å
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Refine LS restraints |
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