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- PDB-3blv: Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulato... -

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Basic information

Entry
Database: PDB / ID: 3blv
TitleYeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits
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 (NAD+) / isocitrate dehydrogenase (NAD+) activity / glutamate biosynthetic process / isocitrate metabolic process / mitochondrial nucleoid / tricarboxylic acid cycle / mitochondrial intermembrane space / NAD binding ...Citric acid cycle (TCA cycle) / : / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / glutamate biosynthetic process / isocitrate metabolic 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
CITRATE ANION / 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 / MAD, MOLECULAR REPLACEMENT / Resolution: 3.2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,05712
Polymers308,3008
Non-polymers7564
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isocitrate dehydrogenase [NAD] subunit 1
B: Isocitrate dehydrogenase [NAD] subunit 2
C: Isocitrate dehydrogenase [NAD] subunit 1
D: Isocitrate dehydrogenase [NAD] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5286
Polymers154,1504
Non-polymers3782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-78 kcal/mol
Surface area51110 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NAD] subunit 1
F: Isocitrate dehydrogenase [NAD] subunit 2
G: Isocitrate dehydrogenase [NAD] subunit 1
H: Isocitrate dehydrogenase [NAD] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5286
Polymers154,1504
Non-polymers3782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-77 kcal/mol
Surface area51240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.899, 112.949, 125.616
Angle α, β, γ (deg.)90.00, 106.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39095.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IDH1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P28834, isocitrate dehydrogenase (NAD+)
#2: Protein
Isocitrate dehydrogenase [NAD] subunit 2 / Isocitric dehydrogenase / NAD(+)-specific ICDH


Mass: 37979.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IDH2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P28241, isocitrate dehydrogenase (NAD+)
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7

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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: 2.83 Å3/Da / Density % sol: 56.56 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.1 M sodium citrate, 0.1 M CHES, 15% ethylene glycol, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97961
ReflectionResolution: 3.2→50 Å / Num. obs: 109531 / % possible obs: 96.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 68.6 Å2 / Rsym value: 0.101 / Net I/σ(I): 11
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 11104 / Rsym value: 0.556 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
PHASERphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: PDB entry 1WPW

1wpw


Resolution: 3.2→49.346 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 5439 5.08 %random
Rwork0.2212 ---
obs0.2235 107063 95.96 %-
Displacement parametersBiso mean: 73.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.337 Å20 Å2-6.8859 Å2
2--33.573 Å20 Å2
3----18.5302 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20801 0 52 0 20853
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.149
LS refinement shellResolution: 3.2→3.2364 Å
RfactorNum. reflection% reflection
Rfree0.3387 167 -
Rwork0.3234 --
obs-3635 96.92 %

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