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

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Basic information

Entry
Database: PDB / ID: 1osi
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 / cytosol
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: 3 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 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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
C: 3-ISOPROPYLMALATE DEHYDROGENASE
D: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)147,3014
Polymers147,3014
Non-polymers00
Water00
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE
C: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)73,6502
Polymers73,6502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-30 kcal/mol
Surface area25080 Å2
MethodPISA
2
B: 3-ISOPROPYLMALATE DEHYDROGENASE
D: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)73,6502
Polymers73,6502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-29 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.500, 86.700, 112.100
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO FUNCTIONAL DIMERS, FORMED BY THE SUBUNITS A AND C, B AND D.

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Components

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


Mass: 36825.160 Da / Num. of mol.: 4
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

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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: 2.72 Å3/Da / Density % sol: 58.2 %
Crystal growpH: 4.8
Details: THE STRUCTURE SOLVED USING CRYSTALS GROWN FROM AMMONIUM SULFATE WAS DEPOSITED AS 1IPD AT PDB. THE CRYSTALLIZATION CONDITION IN THIS STRUCTURE WAS SIMILAR AS THE MUTANT A172L., pH 4.8
Crystal grow
*PLUS
pH: 7.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMpotassium phosphate1drop
26.5 %PEG40001reservoir
30.1 Msodium acetate1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 27930 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 0.927 % / Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata reduction
X-PLOR3.1phasing
RefinementResolution: 3→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.149 -
obs0.149 24207
Displacement parametersBiso mean: 26.2 Å2
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10380 0 0 0 10380
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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