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Yorodumi- PDB-3o80: Crystal structure of monomeric KlHxk1 in crystal form IX (open state) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o80 | ||||||
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Title | Crystal structure of monomeric KlHxk1 in crystal form IX (open state) | ||||||
Components | Hexokinase | ||||||
Keywords | TRANSFERASE / RNASEH-LIKE FOLD / HEXOKINASE / GLYCOLYSIS / GLUCOSE REPRESSION / ATP BINDING / MIG1 BINDING | ||||||
Function / homology | Function and homology information mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion ...mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Kuettner, E.B. / Kettner, K. / Keim, A. / Kriegel, T.M. / Strater, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal Structure of Hexokinase KlHxk1 of Kluyveromyces lactis: A MOLECULAR BASIS FOR UNDERSTANDING THE CONTROL OF YEAST HEXOKINASE FUNCTIONS VIA COVALENT MODIFICATION AND OLIGOMERIZATION. Authors: Kuettner, E.B. / Kettner, K. / Keim, A. / Svergun, D.I. / Volke, D. / Singer, D. / Hoffmann, R. / Muller, E.C. / Otto, A. / Kriegel, T.M. / Strater, N. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and preliminary X-ray diffraction studies of hexokinase KlHxk1 from Kluyveromyces lactis Authors: Kuettner, E.B. / Kriegel, T.M. / Keim, A. / Naumann, M. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o80.cif.gz | 197.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o80.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 3o80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o80_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3o80_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3o80_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 3o80_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/3o80 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/3o80 | HTTPS FTP |
-Related structure data
Related structure data | 3o08SC 3o1bC 3o1wC 3o4wC 3o5bC 3o6wC 3o8mC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53672.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: CBS2359/152 / Gene: KLLA0D11352g, RAG5 / Plasmid: pTSRAG5 / Production host: Kluyveromyces lactis (yeast) / Strain (production host): JA6-delta-rag5 / References: UniProt: P33284, hexokinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.5microL reservoir + 0.5microL protein, reservoir: 1.6M triammonium citrate pH 6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 2mM AMPPCP, crystal soaked in ...Details: 0.5microL reservoir + 0.5microL protein, reservoir: 1.6M triammonium citrate pH 6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 2mM AMPPCP, crystal soaked in 50mM AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2008 Details: 1st mirror: Silicon, active surface 50 nm Rh-coated; 2nd mirror: Glas, active s urface 50 nm Rh-coated |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→30 Å / Num. all: 36671 / Num. obs: 36453 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2656 / Rsym value: 0.506 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O08 Resolution: 2.18→29.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.105 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FULL B FACTORS AND ANISO RECORDS WERE COMPUTED BY CCP4 PROGRAMM TLSANL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.011 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→29.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.236 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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