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- PDB-1v53: The crystal structure of 3-isopropylmalate dehydrogenase from Bac... -

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Basic information

Entry
Database: PDB / ID: 1v53
TitleThe crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / 3-isopropylmalate dehydrogenase / IPMDH / Bacillus coagulans / homo dimer / X-ray analysis
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
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 speciesBacillus coagulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsFujita, K. / Minami, H. / Suzuki, K. / Tsunoda, M. / Sekiguchi, T. / Mizui, R. / Tsuzaki, S. / Nakamura, S. / Takenaka, A.
CitationJournal: To be Published
Title: The crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans
Authors: Fujita, K. / Minami, H. / Suzuki, K. / Tsunoda, M. / Sekiguchi, T. / Mizui, R. / Tsuzaki, S. / Nakamura, S. / Takenaka, A.
History
DepositionNov 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,5112
Polymers79,5112
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-24 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.180, 112.180, 192.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-414-

HOH

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Components

#1: Protein 3-isopropylmalate dehydrogenase /


Mass: 39755.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coagulans (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P12010, 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, sodium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Mar 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.85→43.35 Å / Num. all: 33347 / Num. obs: 33314 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SCALAdata scaling
AMoREphasing
CNSrefinement
d*TREKdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AYQ

2ayq


Resolution: 2.85→43.35 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2495 3273 RANDAM
Rwork0.2063 --
all-32714 -
obs-29441 -
Refinement stepCycle: LAST / Resolution: 2.85→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5404 0 0 145 5549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.36
LS refinement shellResolution: 2.85→2.87 Å
RfactorNum. reflection
Rfree0.366 70
Rwork0.3176 -
obs-549

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