+Open data
-Basic information
Entry | Database: PDB / ID: 3a54 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the A47Q1 mutant of pro-protein-glutaminase | ||||||
Components | Protein-glutaminase | ||||||
Keywords | HYDROLASE / mutant structure like a substrate-enzyme complex | ||||||
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: 1.502 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3a54.cif.gz | 282.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3a54.ent.gz | 231.8 KB | Display | PDB format |
PDBx/mmJSON format | 3a54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a54_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3a54_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 3a54_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 3a54_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/3a54 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/3a54 | HTTPS FTP |
-Related structure data
Related structure data | 2zk9C 3a55C 3a56SC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33611.750 Da / Num. of mol.: 2 / Mutation: A47Q 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 20% PEG 3350, 0.2M ammonium tartrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 6, 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→20 Å / Num. obs: 125864 / % possible obs: 98.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11528 / % possible all: 91.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A56 Resolution: 1.502→19.894 Å / FOM work R set: 0.924 / SU ML: 0.18 / σ(F): 1.89 / Phase error: 13.83 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.854 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.492 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.502→19.894 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
|