+Open data
-Basic information
Entry | Database: PDB / ID: 1leh | ||||||
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Title | LEUCINE DEHYDROGENASE FROM BACILLUS SPHAERICUS | ||||||
Components | LEUCINE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Lysinibacillus sphaericus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Baker, P.J. / Turnbull, A.P. / Sedelnikova, S.E. / Stillman, T.J. / Rice, D.W. | ||||||
Citation | Journal: Structure / Year: 1995 Title: A role for quaternary structure in the substrate specificity of leucine dehydrogenase. Authors: Baker, P.J. / Turnbull, A.P. / Sedelnikova, S.E. / Stillman, T.J. / Rice, D.W. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Quaternary Structure Analysis of the Nad(+)-Dependent Leucine Dehydrogenase from Bacillus Sphaericus Authors: Turnbull, A.P. / Ashford, S.R. / Baker, P.J. / Rice, D.W. / Rodgers, F.H. / Stillman, T.J. / Hanson, R.L. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Evolution of Substrate Diversity in the Superfamily of Amino Acid Dehydrogenases. Prospects for Rational Chiral Synthesis Authors: Britton, K.L. / Baker, P.J. / Engel, P.C. / Rice, D.W. / Stillman, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1leh.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1leh.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 1leh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1leh ftp://data.pdbj.org/pub/pdb/validation_reports/le/1leh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE MULTIMERIC STRUCTURES OF BACILLUS STEAROTHERMOPHILUS LEUDH AND BACILLUS SUBTILIS HAVE BEEN REPORTED AS HEXAMERS ON THE BASIS OF GEL FILTRATION STUDIES; INDEED THE LEUCINE DEHYDROGENASE FROM BACILLUS SPHAERICUS WAS ALSO INITIALLY REPORTED AS A HEXAMER. HOWEVER THE X-RAY STRUCTURE IS MOST DEFINITELY A HOMOOCTAMER AND ON THE BASIS OF THE SEQUENCE IDENTITIES BETWEEN THE LEUDH'S FROM THE OTHER SPECIES, THEN THESE MUST ALL BE OCTAMERS AS WELL. |
-Components
#1: Protein | Mass: 39086.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lysinibacillus sphaericus (bacteria) / References: UniProt: Q7SIB4, EC: 1.4.1.9 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.912 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.912 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.8 Å / Num. obs: 57500 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 |
Reflection | *PLUS Num. obs: 57499 / Num. measured all: 190002 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.201 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.017 |