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Yorodumi- PDB-1ekf: CRYSTALLOGRAPHIC STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ekf | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL) COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE AT 1.95 ANGSTROMS (ORTHORHOMBIC FORM) | ||||||
Components | BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL) | ||||||
Keywords | TRANSFERASE / fold type IV | ||||||
Function / homology | Function and homology information regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism ...regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / amino acid biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Yennawar, N.H. / Dunbar, J.H. / Conway, M. / Hutson, S.M. / Farber, G.K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: The structure of human mitochondrial branched-chain aminotransferase. Authors: Yennawar, N. / Dunbar, J. / Conway, M. / Hutson, S. / Farber, G. #1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1997 Title: Cloning of the Rat and Human Mitochondrial Branched Chain Aminotransferases (BCATm) Authors: Bledsoe, R.K. / Dawson, P.A. / Hutson, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ekf.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ekf.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ekf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ekf_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 1ekf_full_validation.pdf.gz | 492.5 KB | Display | |
Data in XML | 1ekf_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 1ekf_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ekf ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ekf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain A and chain B. |
-Components
#1: Protein | Mass: 41368.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: O15382, branched-chain-amino-acid 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: 2.519 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG1500, HEPES, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 223 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0721203 |
Detector | Detector: CCD / Date: Apr 20, 1999 |
Radiation | Monochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0721203 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→24.29 Å / Num. all: 57217 / Num. obs: 48329 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.81 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.34 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.414 / % possible all: 63.8 |
Reflection shell | *PLUS % possible obs: 63.8 % |
-Processing
Software |
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Refinement | Starting model: E. COLI BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE. Resolution: 1.95→24.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 199264.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh and Huber Details: THE DENSITY FOR LOOP 172 TO 179 IN MONOMER A IS WEAK. THE DENSITY FOR THE SAME LOOP IN MONOMER B IS GOOD.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.13 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→24.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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