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- PDB-5yzi: Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase com... -

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Basic information

Entry
Database: PDB / ID: 5yzi
TitleCrystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase complexed with Cadmium
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / IDH
Function / homology
Function and homology information


NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / isocitrate metabolic process / Peroxisomal protein import / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle ...NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / isocitrate metabolic process / Peroxisomal protein import / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / tricarboxylic acid cycle / Neutrophil degranulation / glutathione metabolic process / response to organic cyclic compound / peroxisome / NAD binding / NADP binding / response to oxidative stress / magnesium ion binding / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.519 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione.
Authors: Cho, H.J. / Cho, H.Y. / Park, J.W. / Kwon, O.S. / Lee, H.S. / Huh, T.L. / Kang, B.S.
History
DepositionDec 14, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 4, 2018ID: 2CMV
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2977
Polymers93,4732
Non-polymers1,8245
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-82 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.246, 91.428, 109.724
Angle α, β, γ (deg.)90.00, 113.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 46736.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Idh1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O88844, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate pH 5.5 ,16% PEG 4000 , 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 29260 / % possible obs: 97.6 % / Redundancy: 3.3 % / Net I/σ(I): 22.7
Reflection shellResolution: 2.5→2.59 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.519→28.866 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.85
RfactorNum. reflection% reflection
Rfree0.2313 1476 5.05 %
Rwork0.1883 --
obs0.1905 29243 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.519→28.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 99 129 6632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046646
X-RAY DIFFRACTIONf_angle_d0.7498990
X-RAY DIFFRACTIONf_dihedral_angle_d6.4413964
X-RAY DIFFRACTIONf_chiral_restr0.047977
X-RAY DIFFRACTIONf_plane_restr0.0041143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5189-2.60020.26641140.23432224X-RAY DIFFRACTION86
2.6002-2.69310.29921120.23542478X-RAY DIFFRACTION94
2.6931-2.80080.28161150.23622480X-RAY DIFFRACTION95
2.8008-2.92810.26561290.23632486X-RAY DIFFRACTION97
2.9281-3.08240.29521330.22032553X-RAY DIFFRACTION98
3.0824-3.27520.26231430.21752560X-RAY DIFFRACTION99
3.2752-3.52770.25341510.19932593X-RAY DIFFRACTION100
3.5277-3.8820.24621410.17452567X-RAY DIFFRACTION99
3.882-4.44190.1841500.16142588X-RAY DIFFRACTION99
4.4419-5.58970.21791430.15952602X-RAY DIFFRACTION100
5.5897-28.86760.18941450.1722636X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19980.3332-0.49631.91030.78413.60170.0108-0.15340.2235-0.0078-0.00740.2873-0.1694-0.4151-0.00120.2340.0462-0.00690.23570.03770.3014-12.39236.412333.2602
21.9752-0.0040.1250.80170.23652.82660.0115-0.387-0.40260.2980.0492-0.16370.54880.4831-0.0370.39570.1559-0.03030.38670.08140.36629.367-4.434836.8547
31.89180.0577-0.6741.51980.97774.1223-0.14730.23610.1468-0.1447-0.03820.33280.2665-0.91290.15230.2232-0.0446-0.00740.42490.02860.3953-18.9976-1.20623.821
41.3248-0.5107-0.7541.17560.31351.1801-0.0847-0.183-0.22020.10740.1707-0.33650.55291.4646-0.08910.45850.37270.00211.21-0.00140.473828.0222-7.975617.4781
51.31270.05750.52330.68920.54315.2353-0.05320.01430.1009-0.04140.0861-0.1574-0.46210.8431-0.04570.2441-0.03570.00240.3220.02330.354412.46039.997423.956
63.18420.2839-0.26021.9201-0.05642.5883-0.14070.0199-0.4763-0.23180.0304-0.14570.72221.00490.08760.56640.34930.03220.782-0.05330.455122.3056-14.60877.3238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 412 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 133 )
5X-RAY DIFFRACTION5chain 'B' and (resid 134 through 285 )
6X-RAY DIFFRACTION6chain 'B' and (resid 286 through 411 )

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