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- PDB-3a55: Crystal structure of the A47Q2 mutant of pro- protein-glutaminase -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a55 | ||||||
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Title | Crystal structure of the A47Q2 mutant of pro- protein-glutaminase | ||||||
![]() | Protein-glutaminase | ||||||
![]() | HYDROLASE / mutant structure like the reaction intermediate | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hashizume, R. / Yamaguchi, S. / Mikami, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.1 KB | Display | ![]() |
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PDB format | ![]() | 221.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 438.9 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zk9C ![]() 3a54C ![]() 3a56SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 33611.750 Da / Num. of mol.: 2 / Mutation: A47Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DH5a / Gene: prgA / Plasmid: pET-20b / Production host: ![]() ![]() References: UniProt: Q9AQQ8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 20% PEG 3350, 0.2M sodium tartrate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 119408 / % possible obs: 93.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.99 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 39.27 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.332 / Num. unique all: 6016 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3A56 Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.497 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 26.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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