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- PDB-1dpz: STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TE... -

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Basic information

Entry
Database: PDB / ID: 1dpz
TitleSTRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD711
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / MINOR GROOVE / PAPERCLIP MOTION
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNurachman, Z. / Akanuma, S. / Sato, T. / Oshima, T. / Tanaka, N.
CitationJournal: Protein Eng. / Year: 2000
Title: Crystal structures of 3-isopropylmalate dehydrogenases with mutations at the C-terminus: crystallographic analyses of structure-stability relationships.
Authors: Nurachman, Z. / Akanuma, S. / Sato, T. / Oshima, T. / Tanaka, N.
History
DepositionDec 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE
B: 3-ISOPROPYLMALATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)74,3292
Polymers74,3292
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-30 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.430, 87.570, 70.890
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-ISOPROPYLMALATE DEHYDROGENASE / IPMDH / IMDH


Mass: 37164.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: LEUB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG400, SODIUM ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 Msodium acetate1drop
210 %(v/v)PEG4001drop
35-7.5 mg/mlprotein1drop
40.1 Msodium acetate1reservoir
520 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→36.1 Å / Num. all: 19530 / Num. obs: 19524 / % possible obs: 57.6 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 616 % / Rmerge(I) obs: 0.34 / % possible all: 14.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 57.6 % / Num. unique obs: 616

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR98.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IPMDH A172L (PDB 1OSJ)

1osj


Resolution: 2.8→6.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / 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
Rfree0.267 1332 10 %RANDOM
Rwork0.177 ---
obs0.177 13270 86.6 %-
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.26 Å
Luzzati d res low-6.8 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.8→6.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 0 69 5248
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_d29.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.69
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.021.5
X-RAY DIFFRACTIONx_mcangle_it3.342
X-RAY DIFFRACTIONx_scbond_it3.062
X-RAY DIFFRACTIONx_scangle_it4.862.5
LS refinement shellResolution: 2.8→2.96 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 1710 10 %
Rwork0.212 1543 -
obs--67.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_TOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3PROTEIN_REP.PARAM
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 98.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.69

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