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Yorodumi- PDB-1tz9: Crystal Structure of the Putative Mannonate Dehydratase from Ente... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tz9 | ||||||
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Title | Crystal Structure of the Putative Mannonate Dehydratase from Enterococcus faecalis, Northeast Structural Genomics Target EfR41 | ||||||
Components | Mannonate dehydratase | ||||||
Keywords | LYASE / alpha-beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Forouhar, F. / Chen, Y. / Xiao, R. / Cooper, B. / Shastry, R. / Acton, T.A. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative Mannonate Dehydratase from Enterococcus faecalis, Northeast Structural Genomics Target EfR41 Authors: Forouhar, F. / Chen, Y. / Xiao, R. / Cooper, B. / Shastry, R. / Acton, T.A. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tz9.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tz9.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tz9_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 1tz9_full_validation.pdf.gz | 474.2 KB | Display | |
Data in XML | 1tz9_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 1tz9_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tz9 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tz9 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42040.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: uxuA / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZC9, mannonate dehydratase #2: 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: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 10% Isopropanol, 10mM DTT, 20% PEG 4k, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.61 Å / Num. all: 29806 / Num. obs: 29389 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.078 / Net I/σ(I): 12.21 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.52 / Num. unique all: 2818 / Rsym value: 0.281 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→29.61 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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