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- PDB-1v94: Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 1v94
TitleCrystal structure of isocitrate dehydrogenase from Aeropyrum pernix
Componentsisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase / 3 layers / alpha/beta/alpha
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / 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
isocitrate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsJeong, J.-J. / Sonoda, T. / Fushinobu, S. / Shoun, H. / Wakagi, T.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix
Authors: Jeong, J.-J. / Sonoda, T. / Fushinobu, S. / Shoun, H. / Wakagi, T.
History
DepositionJan 20, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isocitrate dehydrogenase
B: isocitrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)95,9662
Polymers95,9662
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-38 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.863, 107.863, 172.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a homodimer in the asymmetric uhit with a twofold non-crystallographic symmetry.

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Components

#1: Protein isocitrate dehydrogenase


Mass: 47982.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE0689 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3)
References: UniProt: Q9YE81, isocitrate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG3350, ammonium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 30, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 47317 / Num. obs: 47175 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 31.3
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 4600 / Rsym value: 0.244 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ICD

4icd


Resolution: 2.28→45.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3204284.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2354 5 %RANDOM
Rwork0.215 ---
all0.217 47175 --
obs0.215 47110 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9739 Å2 / ksol: 0.32727 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--1.38 Å20 Å2
3----2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.28→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 0 243 6860
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.951.5
X-RAY DIFFRACTIONc_mcangle_it2.832
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.292.5
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 389 5.1 %
Rwork0.229 7311 -
obs-7700 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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