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Yorodumi- PDB-4eff: Crystal structure of aromatic-amino-acid aminotransferase from Bu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eff | ||||||
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Title | Crystal structure of aromatic-amino-acid aminotransferase from Burkholderia pseudomallei | ||||||
Components | Aromatic-amino-acid aminotransferase | ||||||
Keywords | TRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / structural genomics | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of aromatic-amino-acid aminotransferase from Burkholderia pseudomallei Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Wall, A. / Craig, T. / Staker, B. / Myler, P. / Stewart, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eff.cif.gz | 159 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eff.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 4eff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/4eff ftp://data.pdbj.org/pub/pdb/validation_reports/ef/4eff | HTTPS FTP |
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-Related structure data
Related structure data | 3fslS S: Starting model for refinement |
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Similar structure data | |
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: 45197.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSS0355, tyrB / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q63NE4, aromatic-amino-acid transaminase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Emerald Bio JCSG+ screen: 14.4% PEG8000, 160 mM calcium acetate, 20% glycerol, Bupse.01471.a.A1 PW 34948 at 36.1 mg/mL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2012 |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 34894 / Num. obs: 34726 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 22.96 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 20.49 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2525 / Rsym value: 0.524 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FSL, CHAIN A Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.526 / SU ML: 0.086 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 14.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.9 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -20.93 Å / Origin y: -6.158 Å / Origin z: 13.775 Å
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