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- PDB-3blx: Yeast Isocitrate Dehydrogenase (Apo Form) -

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Basic information

Entry
Database: PDB / ID: 3blx
TitleYeast Isocitrate Dehydrogenase (Apo Form)
Components
  • Isocitrate dehydrogenase [NAD] subunit 1
  • Isocitrate dehydrogenase [NAD] subunit 2
KeywordsOXIDOREDUCTASE / TCA cycle / oxidative metabolism / allostery / dehydrogenase / decarboxylase / Allosteric enzyme / Magnesium / Manganese / Metal-binding / Mitochondrion / NAD / RNA-binding / Transit peptide / Tricarboxylic acid cycle / Phosphoprotein
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / isocitrate metabolic process / glutamate biosynthetic process / mitochondrial nucleoid / tricarboxylic acid cycle / mitochondrial intermembrane space / NAD binding ...Citric acid cycle (TCA cycle) / isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / isocitrate metabolic process / glutamate biosynthetic process / mitochondrial nucleoid / tricarboxylic acid cycle / mitochondrial intermembrane space / NAD binding / mitochondrial matrix / magnesium ion binding / mitochondrion / RNA binding / cytosol
Similarity search - Function
Isocitrate dehydrogenase NAD-dependent / 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 [NAD] subunit 2, mitochondrial / Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTaylor, A.B. / Hu, G. / Hart, P.J. / McAlister-Henn, L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Allosteric Motions in Structures of Yeast NAD+-specific Isocitrate Dehydrogenase.
Authors: Taylor, A.B. / Hu, G. / Hart, P.J. / McAlister-Henn, L.
History
DepositionDec 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 1.3Nov 20, 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 [NAD] subunit 1
B: Isocitrate dehydrogenase [NAD] subunit 2
C: Isocitrate dehydrogenase [NAD] subunit 1
D: Isocitrate dehydrogenase [NAD] subunit 2
E: Isocitrate dehydrogenase [NAD] subunit 1
F: Isocitrate dehydrogenase [NAD] subunit 2
G: Isocitrate dehydrogenase [NAD] subunit 1
H: Isocitrate dehydrogenase [NAD] subunit 2
I: Isocitrate dehydrogenase [NAD] subunit 1
J: Isocitrate dehydrogenase [NAD] subunit 2
K: Isocitrate dehydrogenase [NAD] subunit 1
L: Isocitrate dehydrogenase [NAD] subunit 2
M: Isocitrate dehydrogenase [NAD] subunit 1
N: Isocitrate dehydrogenase [NAD] subunit 2
O: Isocitrate dehydrogenase [NAD] subunit 1
P: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)607,32316
Polymers607,32316
Non-polymers00
Water00
1
A: Isocitrate dehydrogenase [NAD] subunit 1
B: Isocitrate dehydrogenase [NAD] subunit 2
C: Isocitrate dehydrogenase [NAD] subunit 1
D: Isocitrate dehydrogenase [NAD] subunit 2
E: Isocitrate dehydrogenase [NAD] subunit 1
F: Isocitrate dehydrogenase [NAD] subunit 2
G: Isocitrate dehydrogenase [NAD] subunit 1
H: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)303,6628
Polymers303,6628
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Isocitrate dehydrogenase [NAD] subunit 1
J: Isocitrate dehydrogenase [NAD] subunit 2
K: Isocitrate dehydrogenase [NAD] subunit 1
L: Isocitrate dehydrogenase [NAD] subunit 2
M: Isocitrate dehydrogenase [NAD] subunit 1
N: Isocitrate dehydrogenase [NAD] subunit 2
O: Isocitrate dehydrogenase [NAD] subunit 1
P: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)303,6628
Polymers303,6628
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Isocitrate dehydrogenase [NAD] subunit 1
B: Isocitrate dehydrogenase [NAD] subunit 2
C: Isocitrate dehydrogenase [NAD] subunit 1
D: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)151,8314
Polymers151,8314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-78 kcal/mol
Surface area51910 Å2
MethodPISA
4
E: Isocitrate dehydrogenase [NAD] subunit 1
F: Isocitrate dehydrogenase [NAD] subunit 2
G: Isocitrate dehydrogenase [NAD] subunit 1
H: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)151,8314
Polymers151,8314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-78 kcal/mol
Surface area51580 Å2
MethodPISA
5
I: Isocitrate dehydrogenase [NAD] subunit 1
J: Isocitrate dehydrogenase [NAD] subunit 2
K: Isocitrate dehydrogenase [NAD] subunit 1
L: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)151,8314
Polymers151,8314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-75 kcal/mol
Surface area51490 Å2
MethodPISA
6
M: Isocitrate dehydrogenase [NAD] subunit 1
N: Isocitrate dehydrogenase [NAD] subunit 2
O: Isocitrate dehydrogenase [NAD] subunit 1
P: Isocitrate dehydrogenase [NAD] subunit 2


Theoretical massNumber of molelcules
Total (without water)151,8314
Polymers151,8314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-80 kcal/mol
Surface area50450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.444, 115.208, 159.247
Angle α, β, γ (deg.)111.03, 96.08, 107.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Isocitrate dehydrogenase [NAD] subunit 1 / EC 1.1.1.41 / Isocitric dehydrogenase / NAD(+)-specific ICDH


Mass: 38076.352 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IDH1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28834, isocitrate dehydrogenase (NAD+)
#2: Protein
Isocitrate dehydrogenase [NAD] subunit 2 / EC 1.1.1.41 / Isocitric dehydrogenase / NAD(+)-specific ICDH


Mass: 37839.027 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IDH2 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28241, isocitrate dehydrogenase (NAD+)
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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 16% polyethylene glycol 3350, 0.13 M potassium sulfate, 0.2 M trimethylamine-N-oxide, 15% propanediol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 185029 / % possible obs: 96.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 71.3 Å2 / Rsym value: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 18017 / Rsym value: 0.554 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BLV

3blv


Resolution: 2.7→35.739 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 9219 5.03 %random
Rwork0.2394 ---
obs0.2407 183432 96.48 %-
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-33.2784 Å2-0.6078 Å21.0639 Å2
2--37.3134 Å2-2.0874 Å2
3---18.834 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41336 0 0 0 41336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_deg1.275
LS refinement shellResolution: 2.7→2.7307 Å
RfactorNum. reflection% reflection
Rfree0.3938 300 -
Rwork0.3482 --
obs-5900 97.38 %

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