+Open data
-Basic information
Entry | Database: PDB / ID: 3a56 | ||||||
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Title | Crystal structure of pro- protein-glutaminase | ||||||
Components | Protein-glutaminase | ||||||
Keywords | HYDROLASE / pro-enzyme | ||||||
Function / homology | Function and homology information OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #340 / Protein glutaminase / Glutaminase / C8orf32 fold - #30 / C8orf32 fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Chryseobacterium proteolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.728 Å | ||||||
Authors | Hashizume, R. / Yamaguchi, S. / Mikami, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structures of protein glutaminase and its pro forms converted into enzyme-substrate complex Authors: Hashizume, R. / Maki, Y. / Mizutani, K. / Takahashi, N. / Matsubara, H. / Sugita, A. / Sato, K. / Yamaguchi, S. / Mikami, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a56.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a56.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 3a56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a56_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 3a56_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 3a56_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 3a56_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/3a56 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/3a56 | HTTPS FTP |
-Related structure data
Related structure data | 2zk9SC 3a54C 3a55C 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: 33554.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chryseobacterium proteolyticum (bacteria) Strain: DH5a / Gene: prgA / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9AQQ8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #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: 2.89 Å3/Da / Density % sol: 57.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 0.2M Ammonium Citrate dibasic, 20% PEG 3350, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.728→50 Å / Num. obs: 80701 / % possible obs: 98.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.35 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.314 / Num. unique all: 7359 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZK9 Resolution: 1.728→30.551 Å / FOM work R set: 0.866 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 496.81 Å2 / Biso mean: 29.611 Å2 / Biso min: 4.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.728→30.551 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29
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