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Yorodumi- PDB-3out: Crystal structure of glutamate racemase from Francisella tularens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3out | ||||||
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Title | Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate. | ||||||
Components | Glutamate racemase | ||||||
Keywords | ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutamate racemase / MurI / Cell envelope / Francisella tularensis subsp. tularensis SCHU S4 / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Function / homology | Function and homology information glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Filippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Kudriska, M. / Edwards, A. / Savchenko, A. / Anderson, F.W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate. Authors: Filippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Kudriska, M. / Edwards, A. / Savchenko, A. / Anderson, F.W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3out.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3out.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 3out.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/3out ftp://data.pdbj.org/pub/pdb/validation_reports/ou/3out | HTTPS FTP |
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-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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29939.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Gene: FTT_1197c, murI / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5NFN6, glutamate racemase #2: Chemical | #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: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 25% PEG 3350, 0.1 M Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR CCD / Detector: CCD / Date: Aug 13, 2010 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25.2 Å / Num. all: 172747 / Num. obs: 172747 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.71 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 11 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.16 / Num. unique all: 9026 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→25.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.687 / SU ML: 0.058 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.396 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→25.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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