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- PDB-1wal: 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) MUTANT (M219A)FROM THERMU... -

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Basic information

Entry
Database: PDB / ID: 1wal
Title3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) MUTANT (M219A)FROM THERMUS THERMOPHILUS
ComponentsPROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / LEUCINE BIOSYNTHESIS / NAD-DEPENDANT ENZYME
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1.0May 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)


Theoretical massNumber of molelcules
Total (without water)36,6951
Polymers36,6951
Non-polymers00
Water1,74797
1
A: PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)

A: PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)


Theoretical massNumber of molelcules
Total (without water)73,3902
Polymers73,3902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4180 Å2
ΔGint-33 kcal/mol
Surface area25320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.400, 78.400, 158.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 36694.926 Da / Num. of mol.: 1 / Mutation: M219A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: LEUB / Plasmid: PET21C LEUB / Species (production host): Escherichia coli / Gene (production host): LEUB / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61495
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.7 Å3/Da / Density % sol: 67.82 %
Crystal growpH: 7.6 / Details: 6 MG/ML PROTEIN IN 1.4 M AMMONIUM SULFATE, pH 7.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
21.4 Mammonium sulfate1drop
320 mM1dropKPO4

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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: 2.27→30 Å / Num. obs: 54255 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.055
Reflection
*PLUS
Num. obs: 22587 / Num. measured all: 54255 / Rmerge(I) obs: 0.055

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Processing

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

1ipd


Resolution: 2.27→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.184 --
obs-22587 84 %
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.27→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 0 97 2684
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_deg1.3
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24 Å2
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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