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Yorodumi- PDB-3tcm: Crystal Structure of Alanine Aminotransferase from Hordeum vulgare -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tcm | ||||||
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Title | Crystal Structure of Alanine Aminotransferase from Hordeum vulgare | ||||||
Components | Alanine aminotransferase 2 | ||||||
Keywords | TRANSFERASE / aminotransferase / Pyridoxal phosphate (PLP)-binding | ||||||
Function / homology | Function and homology information alanine transaminase / L-alanine:2-oxoglutarate aminotransferase activity / L-alanine catabolic process / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Rydel, T.J. / Sturman, E.J. / Halls, C. / Chen, S. / Zeng, J. / Evdokimov, A. / Duff, S.M.G. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2012 Title: The Enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the HvAlaAT crystal structure. Authors: Duff, S.M. / Rydel, T.J. / McClerren, A.L. / Zhang, W. / Li, J.Y. / Sturman, E.J. / Halls, C. / Chen, S. / Zeng, J. / Peng, J. / Kretzler, C.N. / Evdokimov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tcm.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tcm.ent.gz | 155.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/3tcm ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tcm | HTTPS FTP |
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-Related structure data
Related structure data | 1xi9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55203.531 Da / Num. of mol.: 2 / Mutation: K119H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: pet24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52894, alanine transaminase #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: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: The protein sample was 12 mg/mL in 20 mM carbonate buffer-pH 10.5, 2.5 mM PLP, 2.5 mM cycloserine, and 2.5 mM DTT. Crystals were obtained using a 0.7 mL well composition of 22(w/v)% ...Details: The protein sample was 12 mg/mL in 20 mM carbonate buffer-pH 10.5, 2.5 mM PLP, 2.5 mM cycloserine, and 2.5 mM DTT. Crystals were obtained using a 0.7 mL well composition of 22(w/v)% polyethylene glycol monomethyl ether (PGME) 5000, 0.1 M MES, 9 (v/v) % tacsimate and a 2 uL sitting drop prepared from equal volumes of protein and well solution., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2009 |
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR WITH HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→87.2 Å / Num. all: 32022 / Num. obs: 31088 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.46 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The phasing template was prepared by the CCP4 program chainsaw from the Pyrococcus furiosis Pfu-1397077-001 (PDB entry 1xi9) coordinate file and the Hv (i.e., barley) AlaAT-PfAlaAT sequence alignment. Resolution: 2.71→87.16 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.172 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 36.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→87.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.781 Å / Total num. of bins used: 20
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