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Yorodumi- PDB-1kt8: HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL):... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kt8 | ||||||
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Title | HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL): THREE DIMENSIONAL STRUCTURE OF ENZYME IN ITS KETIMINE FORM WITH THE SUBSTRATE L-ISOLEUCINE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yennawar, N.H. / Conway, M.E. / Yennawar, H.P. / Farber, G.K. / Hutson, S.M. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms Authors: Yennawar, N.H. / Conway, M.E. / Yennawar, H.P. / Farber, G.K. / Hutson, S.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: The Structure of Human Mitochondrial Branched-Chain Aminotransferase Authors: Yennawar, N.H. / Dunbar, J. / Conway, M. / Hutson, S.M. / Farber, G.K. #2: Journal: Biochim.Biophys.Acta / Year: 1997 Title: Cloning of the Rat and Human Mitochondrial Branched Amino Acid Aminotransferase (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 | 1kt8.cif.gz | 162.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kt8.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kt8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1kt8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1kt8_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 1kt8_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kt8 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kt8 | HTTPS FTP |
-Related 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: 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: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-GOL / | #5: 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: 2.38 Å3/Da / Density % sol: 48.25 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: PEG1500, HEPES, DTT, pH 7.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Yennawar, N., (2001) Acta Crystallogr., Sect.D, 57, 506. | ||||||||||||||||||||||||||||||||||||||||
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: 1.9→19.72 Å / Num. all: 61893 / Num. obs: 60100 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.66 / % possible all: 41 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 19.7 Å / Num. obs: 61939 / Redundancy: 4.7 % / Num. measured all: 238575 |
Reflection shell | *PLUS % possible obs: 90.3 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2356223.4 / Data cutoff high rms absF: 2356223.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.197 Å2 / ksol: 0.320221 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 19.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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