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- PDB-1leh: LEUCINE DEHYDROGENASE FROM BACILLUS SPHAERICUS -

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Basic information

Entry
Database: PDB / ID: 1leh
TitleLEUCINE DEHYDROGENASE FROM BACILLUS SPHAERICUS
ComponentsLEUCINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


leucine dehydrogenase / oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / branched-chain amino acid catabolic process / nucleotide binding
Similarity search - Function
Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ...Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Leucine dehydrogenase
Similarity search - Component
Biological speciesLysinibacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBaker, 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
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Other
Category: pdbx_database_status / pdbx_struct_assembly_auth_evidence
Item: _pdbx_database_status.process_site
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCINE DEHYDROGENASE
B: LEUCINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)78,1722
Polymers78,1722
Non-polymers00
Water2,090116
1
A: LEUCINE DEHYDROGENASE
B: LEUCINE DEHYDROGENASE

A: LEUCINE DEHYDROGENASE
B: LEUCINE DEHYDROGENASE

A: LEUCINE DEHYDROGENASE
B: LEUCINE DEHYDROGENASE

A: LEUCINE DEHYDROGENASE
B: LEUCINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)312,6908
Polymers312,6908
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area27960 Å2
ΔGint-36 kcal/mol
Surface area103500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.400, 138.400, 121.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.514069, 0.857679, 0.01096), (0.857709, -0.514126, 0.003026), (0.00823, 0.007845, -0.999935)0.01877, 0.08177, 0.93003
2given(0.514069, 0.857679, 0.01096), (0.857709, -0.514126, 0.003026), (0.00823, 0.007845, -0.999935)0.01877, 0.08177, 0.93003
DetailsTHE 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.

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Components

#1: Protein LEUCINE DEHYDROGENASE


Mass: 39086.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lysinibacillus sphaericus (bacteria) / References: UniProt: Q7SIB4, leucine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 60 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
20.1 MMES-NaOH1drop
31 mMEDTA1drop
41.8-2.1 Mammonium sulfate1reservoir
50.1 MMES-NaOH1reservoir
61 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
RefinementResolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.201 --
all-56941 -
obs-56941 97 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 0 116 5604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.095
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.017
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
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

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