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- PDB-1gc9: THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE D... -

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Basic information

Entry
Database: PDB / ID: 1gc9
TitleTHE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO GLY
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / IPMDH / IMDH / Thermostability / dehydrogenation / decarboxylation
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: 2.3 Å
AuthorsQu, C. / Akanuma, S. / Tanaka, N. / Moriyama, H. / Oshima, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Design, X-ray crystallography, molecular modelling and thermal stability studies of mutant enzymes at site 172 of 3-isopropylmalate dehydrogenase from Thermus thermophilus.
Authors: Qu, C. / Akanuma, S. / Tanaka, N. / Moriyama, H. / Oshima, T.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,8111
Polymers36,8111
Non-polymers00
Water99155
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE

A: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)73,6222
Polymers73,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4200 Å2
ΔGint-29 kcal/mol
Surface area25130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.610, 78.610, 158.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer constructed by chain A and a symetry partner generated by the two-fold axis.

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Components

#1: Protein 3-ISOPROPYLMALATE DEHYDROGENASE


Mass: 36811.133 Da / Num. of mol.: 1 / Mutation: A172G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: LEUB / Plasmid: JA221 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.7 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Ammonuim sulfate, potassium phosphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Sakurai, M., (1992) J.Biochem., 112, 173. / PH range low: 8.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMpotassium phosphate1droppH7.6
31.0-2.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 16105 / % possible obs: 88.5 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.064
Reflection
*PLUS
Rmerge(I) obs: 0.0638

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementResolution: 2.3→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2474507.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1600 9.9 %RANDOM
Rwork0.173 ---
obs0.173 16105 88.5 %-
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-6 Å
Luzzati sigma a0.38 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 0 55 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it2.541.5
X-RAY DIFFRACTIONc_mcangle_it3.762
X-RAY DIFFRACTIONc_scbond_it22.272
X-RAY DIFFRACTIONc_scangle_it19.212.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 174 10.6 %
Rwork0.253 1474 -
obs--41.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.PARAM
X-RAY DIFFRACTION4PROTEIN.LINK
X-RAY DIFFRACTION5WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.9 % / Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Rfactor obs: 0.173 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.387
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.34
X-RAY DIFFRACTIONc_mcbond_it2.541.5
X-RAY DIFFRACTIONc_scbond_it22.272
X-RAY DIFFRACTIONc_mcangle_it3.762
X-RAY DIFFRACTIONc_scangle_it19.212.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.253

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