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- PDB-1cm7: 3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1cm7
Title3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI
ComponentsPROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / NAD-DEPENDANT ENZYME / LEUCINE BIOSYNTHETIC PATHWAY
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / cellular response to amino acid starvation / NAD binding / manganese ion binding / magnesium ion binding / metal ion 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsWallon, G. / Kryger, G. / Lovett, S.T. / Oshima, T. / Ringe, D. / Petsko, G.A.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus.
Authors: Wallon, G. / Kryger, G. / Lovett, S.T. / Oshima, T. / Ringe, D. / Petsko, G.A.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)
B: PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)


Theoretical massNumber of molelcules
Total (without water)79,1202
Polymers79,1202
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-29 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 86.900, 83.700
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE) / IPMDH / IMDH


Mass: 39559.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LEUB / Plasmid: pWallyI / Species (production host): Escherichia coli / Gene (production host): LEUB / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30125
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.8 Å3/Da / Density % sol: 51.94 %
Crystal growpH: 7.5
Details: 15 MG/ML PROTEIN IN 15% PEG 4K, 50 MM TRIS PH = 7.5, 0.35 M MGCL2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215 %(w/v)PEG40001reservoir
350 mMTris-HCl1reservoir
40.35 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 36432 / % possible obs: 0.79 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.058
Reflection
*PLUS
% possible obs: 79 % / Num. measured all: 89369 / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1 IPD

Resolution: 2.06→6 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.173 ---
obs-89369 79 %-
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 2.06→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 0 231 5753
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_deg1.7
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
Refine LS restraints NCSNCS model details: RESTRAINTS

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