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Yorodumi- PDB-3agd: Crystal structure of Mglu in its native form in the presence of 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3agd | ||||||
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Title | Crystal structure of Mglu in its native form in the presence of 4.3M NaCl | ||||||
Components | Salt-tolerant glutaminase | ||||||
Keywords | HYDROLASE / Glutaminase super family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Micrococcus luteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yoshimune, K. / Shirakihara, Y. / Yumoto, I. | ||||||
Citation | Journal: To be Published Title: Salt-induced conformational change of salt-tolerant glutaminase from Micrococcus luteus K-3 Authors: Yoshimune, K. / Shirakihara, Y. / Yumoto, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3agd.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3agd.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 3agd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/3agd ftp://data.pdbj.org/pub/pdb/validation_reports/ag/3agd | HTTPS FTP |
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-Related structure data
Related structure data | 3ageC 3agfC 3if5S 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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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: 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: 2.95 Å3/Da / Density % sol: 58.31 % |
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Crystal grow | Temperature: 293 K / Method: microbatch method / pH: 7.5 Details: 10mg/ml protein, 50mM HEPES, 1M ammonium formate, 4.3M NaCl, pH 7.5, Microbatch method, 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: Jun 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→62.3 Å / Num. all: 58860 / Num. obs: 58857 / % possible obs: 100 % / Observed criterion σ(I): 4.8 / Redundancy: 6.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.8 / Num. unique all: 8473 / Rsym value: 0.381 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3if5 Resolution: 2.2→59.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.493 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→59.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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