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Yorodumi- PDB-3giq: Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3giq | ||||||
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Title | Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate. | ||||||
Components | N-acyl-D-glutamate deacylase | ||||||
Keywords | HYDROLASE / N-acyl-D-Glutamate Deacylase / amidohydrolase / reaction intermediate | ||||||
Function / homology | Function and homology information N-acyl-D-glutamate deacylase / N-acyl-D-glutamate deacylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily. Authors: Cummings, J.A. / Fedorov, A.A. / Xu, C. / Brown, S. / Fedorov, E. / Babbitt, P.C. / Almo, S.C. / Raushel, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3giq.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3giq.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 3giq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3giq ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3giq | HTTPS FTP |
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-Related structure data
Related structure data | 3gipSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
#1: Protein | Mass: 51177.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB3285 / Production host: Escherichia coli (E. coli) References: UniProt: Q7WHC3, UniProt: A0A0H3LXD5*PLUS, N-acyl-D-glutamate deacylase #2: Chemical | #3: Chemical | ChemComp-ZN / #4: 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: 2.98 Å3/Da / Density % sol: 58.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.0M ammonium phosphate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 106991 / Num. obs: 106991 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GIP Resolution: 1.8→24.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2986212 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.5806 Å2 / ksol: 0.386359 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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