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Yorodumi- PDB-1kq3: CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kq3 | ||||||
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Title | CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION | ||||||
Components | glycerol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / GLYCEROL DEHYDROGENASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI | ||||||
Function / homology | Function and homology information anaerobic glycerol catabolic process / glycerol dehydrogenase (NAD+) activity / glycerol dehydrogenase / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Wilson, I.A. / Miller, M.D. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. ...Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. / McPhillips, T.M. / Miller, M.A. / Scheibe, D. / Canaves, J.M. / Guda, C. / Jaroszewski, L. / Selby, T.L. / Elsliger, M.-A. / Wooley, J. / Taylor, S.S. / Hodgson, K.O. / Wilson, I.A. / Schultz, P.G. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kq3.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kq3.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kq3_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 1kq3_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 1kq3_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 1kq3_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kq3 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kq3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The functional molecule is a monomer. The coordinates describe the asymmetric unit. |
-Components
#1: Protein | Mass: 41198.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0423 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WYQ4 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-TRS / |
#5: 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: 2.3 Å3/Da / Density % sol: 46.59 % |
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Crystal grow | Temperature: 293 K / pH: 6.2 Details: 35% MPD, 0.1M Na/k phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.20 |
Crystal grow | *PLUS Method: vapor diffusion, sitting drop |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 2001 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 61417 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.044 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.234 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 |
Reflection shell | *PLUS Redundancy: 4.5 % / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→20 Å / σ(F): 2 Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH & HUBER
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Displacement parameters | Biso mean: 16.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |