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Yorodumi- PDB-4h19: Crystal structure of an enolase (mandelate racemase subgroup, tar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h19 | ||||||
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Title | Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop | ||||||
Components | Mandelate racemase | ||||||
Keywords | LYASE / Enolase / mandelate racemase subgroup / enzyme function initiative / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Vetting, M.W. / Bouvier, J.T. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop Authors: Vetting, M.W. / Bouvier, J.T. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h19.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4h19.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4h19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/4h19 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/4h19 | HTTPS FTP |
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-Related structure data
Related structure data | 3tj4S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 16 molecules ABCDEFGHIKLMNPJO
#1: Protein | Mass: 41123.445 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: Atu4120 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CU39 |
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-Non-polymers , 6 types, 5928 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-0YR / ( #7: 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: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 298 K / Method: sitting drop vapor diffuction / pH: 4 Details: Protein (10 mM Tris, pH 8.0, 200 mM NaCl, 5 mM Mg, 10 mM D-ribonohydroxamate; Reservoir (20% (w/v) PEG-8000, 100 mM Tris pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir, + 20% glycerol, 50 ...Details: Protein (10 mM Tris, pH 8.0, 200 mM NaCl, 5 mM Mg, 10 mM D-ribonohydroxamate; Reservoir (20% (w/v) PEG-8000, 100 mM Tris pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir, + 20% glycerol, 50 mM MgCl, 10 mM D-ribonohydroxamate), sitting drop vapor diffuction, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 11, 2011 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→197.844 Å / Num. all: 573535 / Num. obs: 573535 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.133 / Net I/σ(I): 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TJ4 Resolution: 1.8→197.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 2.173 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 92.84 Å2 / Biso mean: 17.366 Å2 / Biso min: 6.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→197.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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