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- PDB-1osj: STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1osj
TitleSTRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Isopropylmalate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsQu, C. / Akanuma, S. / Moriyama, H. / Tanaka, N. / Oshima, T.
Citation
Journal: Protein Eng. / Year: 1997
Title: A mutation at the interface between domains causes rearrangement of domains in 3-isopropylmalate dehydrogenase.
Authors: Qu, C. / Akanuma, S. / Moriyama, H. / Tanaka, N. / Oshima, T.
#1: Journal: J.Biochem.(Tokyo) / Year: 1990
Title: Purification, Catalytic Properties, and Thermal Stability of Threo-Ds-3-Isopropylmalate Dehydrogenase Coded by Leub Gene from an Extreme Thermophile, Thermus Thermophilus Strain Hb8
Authors: Yamada, T. / Akutsu, N. / Miyazaki, K. / Kakinuma, K. / Yoshida, M. / Oshima, T.
History
DepositionOct 22, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE
B: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)73,7342
Polymers73,7342
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-27 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 88.100, 72.000
Angle α, β, γ (deg.)90.00, 100.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-ISOPROPYLMALATE DEHYDROGENASE / / IPMDH / IMDH


Mass: 36867.238 Da / Num. of mol.: 2 / Mutation: A172L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: unidentified (others)
References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.6 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMpotassium phosphate1drop
23 %PEG40001reservoir
30.1 Msodium acetate1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 23, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 26811 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 0.938 % / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.35→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.178 -
obs0.178 24963
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 0 69 5265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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