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Yorodumi- PDB-1te5: The 2.0 Angstrom crystal structure of predicted glutamine amidotr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1te5 | ||||||
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Title | The 2.0 Angstrom crystal structure of predicted glutamine amidotransferase from Pseudomonas aeruginosa PA01 | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | UNKNOWN FUNCTION / glutamine amidotransferase / amidotransferase / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase EgtC-like / Glutamine amidotransferases class-II / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Patskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of amidophosphoribosyltransferase from Pseudomonas aeruginosa Authors: Patskovsky, Y. / Almo, S.C. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1te5.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1te5.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 1te5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1te5_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
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Full document | 1te5_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 1te5_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 1te5_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1te5 ftp://data.pdbj.org/pub/pdb/validation_reports/te/1te5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28575.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PAO1 / Gene: PA1307 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I437 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow | Temperature: 280 K / pH: 7.5 Details: 0.1M HEPES, 28% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K, pH 7.50 |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 | |||||||||||||||
Detector |
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Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 32917 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 29.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.7 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.32 / % possible all: 43.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 300000 / Data cutoff low absF: 0.01 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.9525 Å2 / ksol: 0.319038 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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