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Yorodumi- PDB-2uyg: Crystallogaphic structure of the typeII 3-Dehydroquinase from The... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uyg | ||||||
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Title | Crystallogaphic structure of the typeII 3-Dehydroquinase from Thermus Thermophilus | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE / TYPEII 3-DEHYDROQUINASE | ||||||
Function / homology | Function and homology information 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Utsunomiya, H. / Agari, Y. / Imagawa, T. / Tsuge, H. | ||||||
Citation | Journal: To be Published Title: Crystallogaphic Structure of the Typeii 3-Dehydroquinase from Thermus Thermophilus Authors: Utsunomiya, H. / Agari, Y. / Imagawa, T. / Tsuge, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uyg.cif.gz | 328.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uyg.ent.gz | 271.4 KB | Display | PDB format |
PDBx/mmJSON format | 2uyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uyg_validation.pdf.gz | 550.7 KB | Display | wwPDB validaton report |
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Full document | 2uyg_full_validation.pdf.gz | 643.9 KB | Display | |
Data in XML | 2uyg_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 2uyg_validation.cif.gz | 91.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyg ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyg | HTTPS FTP |
-Related structure data
Related structure data | 1gqoS S: Starting model for refinement |
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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: 16468.775 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): B834(DE3) / References: UniProt: Q5SIL5, 3-dehydroquinate dehydratase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.1 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.8M AMM3CITRATE,0.1M BIS-TRIS PEOPANE(PH7) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 |
Detector | Type: JUPITER 210 / Detector: CCD / Date: Oct 19, 2004 Details: A FIXED EXIT SI DOUBLE CRYSTAL MONOCHROMATOR FOLLOWED BY A TWO DIMENSIONAL FOCUSING MIRROR WHICH IS COATED IN RHODIUM. |
Radiation | Monochromator: SI DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.2 Å / Num. obs: 103688 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.29 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GQO Resolution: 2.2→48.22 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.841 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURAL GENOMICS PROJECT NAME NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES STRUCTURAL GENOMICS PROJECT CENTER ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURAL GENOMICS PROJECT NAME NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES STRUCTURAL GENOMICS PROJECT CENTER NAME RIKEN STRUCTURAL GENOMICS PROTEOMICS INITIATIVE
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.22 Å
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Refine LS restraints |
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