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- PDB-8w49: mouse isocitrate dehydrogenase with isocitrate and magnesium -

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Basic information

Entry
Database: PDB / ID: 8w49
Titlemouse isocitrate dehydrogenase with isocitrate and magnesium
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase enzyme-substrate complex oxidoreductase homodimer
Function / homology
Function and homology information


NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / Peroxisomal protein import / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / female gonad development / NADPH regeneration / 2-oxoglutarate metabolic process ...NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / Peroxisomal protein import / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / female gonad development / NADPH regeneration / 2-oxoglutarate metabolic process / glyoxylate cycle / response to steroid hormone / peroxisomal matrix / tricarboxylic acid cycle / Neutrophil degranulation / glutathione metabolic process / NAD binding / NADP binding / response to oxidative stress / magnesium ion binding / protein homodimerization activity / mitochondrion / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
ISOCITRIC ACID / ISOPROPYL ALCOHOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKang, B.S. / Cho, H.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015R1A4A1042271 Korea, Republic Of
CitationJournal: To Be Published
Title: mouse isocitrate dehydrogenase with isocitrate and magnesium
Authors: Kang, B.S. / Cho, H.Y.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,46222
Polymers186,9464
Non-polymers3,51718
Water27,3831520
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,63312
Polymers93,4732
Non-polymers2,16010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-50 kcal/mol
Surface area30010 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82910
Polymers93,4732
Non-polymers1,3578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-46 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.627, 93.448, 111.275
Angle α, β, γ (deg.)90.000, 113.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 46736.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Idh1 / Production host: Escherichia coli (E. coli)
References: UniProt: O88844, isocitrate dehydrogenase (NADP+)

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Non-polymers , 5 types, 1538 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1520 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, sodium citrate, magnesium chloride, isocitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→33.9 Å / Num. obs: 180017 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.34 Å2 / CC1/2: 0.992 / Net I/σ(I): 26
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 8502 / CC1/2: 0.414

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→33.9 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 20.3994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 1946 1.13 %
Rwork0.1695 170772 -
obs0.1699 172718 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.08 Å2
Refinement stepCycle: LAST / Resolution: 1.77→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12986 0 228 1520 14734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007513484
X-RAY DIFFRACTIONf_angle_d0.979618200
X-RAY DIFFRACTIONf_chiral_restr0.05821967
X-RAY DIFFRACTIONf_plane_restr0.00742323
X-RAY DIFFRACTIONf_dihedral_angle_d8.98481916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.25591100.224310476X-RAY DIFFRACTION82.9
1.81-1.860.24591310.206311414X-RAY DIFFRACTION90.14
1.86-1.920.19511320.196511605X-RAY DIFFRACTION91.75
1.92-1.980.2631370.196611900X-RAY DIFFRACTION93.97
1.98-2.050.23921480.195212214X-RAY DIFFRACTION96.56
2.05-2.130.24941440.182312383X-RAY DIFFRACTION97.82
2.13-2.230.2091400.170812408X-RAY DIFFRACTION98.01
2.23-2.350.20131430.166312508X-RAY DIFFRACTION98.28
2.35-2.490.23441410.173212435X-RAY DIFFRACTION98.3
2.49-2.690.21631390.174812580X-RAY DIFFRACTION98.94
2.69-2.960.21211500.172412604X-RAY DIFFRACTION99.14
2.96-3.380.17891410.163212680X-RAY DIFFRACTION99.37
3.38-4.260.1831470.146112704X-RAY DIFFRACTION99.51
4.26-33.90.17711430.157112861X-RAY DIFFRACTION99.34

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