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- PDB-1idm: 3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA -

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Basic information

Entry
Database: PDB / ID: 1idm
Title3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHIMERA
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 / 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 / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSakurai, M. / Ohzeki, M. / Moriyama, H. / Sato, M. / Tanaka, N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of a loop-deleted variant of 3-isopropylmalate dehydrogenase from Thermus thermophilus: an internal reprieve tolerance mechanism.
Authors: Sakurai, M. / Ohzeki, M. / Miyazaki, K. / Moriyama, H. / Sato, M. / 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
DepositionMay 19, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)36,4721
Polymers36,4721
Non-polymers00
Water1,964109
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE

A: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)72,9432
Polymers72,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4260 Å2
ΔGint-28 kcal/mol
Surface area24930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.450, 78.450, 158.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO 141

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Components

#1: Protein 3-ISOPROPYLMALATE DEHYDROGENASE / IPMDH


Mass: 36471.656 Da / Num. of mol.: 1 / Mutation: LOOP-DELETED MUTANT, ARG 82 AND LYS 83 DELETED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8
Description: HYBRID BETWEEN THERMUS IPMDH (332 RESIDUES) AND YEAST IPMDH (11 RESIDUES)
Production host: Escherichia coli (E. coli) / Strain (production host): JA221
References: UniProt: P00351, UniProt: Q5SIY4*PLUS, 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.6 / Details: Sakurai, M., (1992) J.Biochem., 112, 173.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMpotassium phosphate1drop
31.0-2.0 Mammonium sulfate1reservoir
420 mMpotassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 26, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 27190 / % possible obs: 76 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.038
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 9999 Å / Num. measured all: 44526 / Rmerge(I) obs: 0.0379

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
PROCESSdata reduction
RefinementResolution: 2.2→5 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 20014 76 %
Displacement parametersBiso mean: 32 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 109 2679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.344
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.344

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