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Yorodumi- PDB-3ihb: Crystal Structure Analysis of Mglu in its tris and glutamate form -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ihb | ||||||
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Title | Crystal Structure Analysis of Mglu in its tris and glutamate form | ||||||
Components | Salt-tolerant glutaminase | ||||||
Keywords | HYDROLASE / Salt-tolerant glutaminase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Micrococcus luteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Yoshimune, K. / Shirakihara, Y. | ||||||
Citation | Journal: Febs J. / Year: 2010 Title: Crystal structure of salt-tolerant glutaminase from Micrococcus luteus K-3 in the presence and absence of its product l-glutamate and its activator Tris Authors: Yoshimune, K. / Shirakihara, Y. / Wakayama, M. / Yumoto, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ihb.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ihb.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ihb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/3ihb ftp://data.pdbj.org/pub/pdb/validation_reports/ih/3ihb | HTTPS FTP |
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-Related structure data
Related structure data | 3if5C 3ih8SC 3ih9C 3ihaC C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48303.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: K-3 / Gene: Glutaminase / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q4U1A6, glutaminase #2: Chemical | #3: Chemical | #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: 3.16 Å3/Da / Density % sol: 61.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 15% PEG 4000, 100mM Sodium Acetate, 50mM HEPES, 300mM Tris, 200mM Glutamate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→57.073 Å / Num. obs: 46819 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.412 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IH8 Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.67 / Data cutoff high absF: 2131955 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.711 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.63 Å2 / Biso mean: 40.938 Å2 / Biso min: 7.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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