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- PDB-6kdy: Crystal structure of the alpha bata heterodimer of human IDH3 in ... -

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Basic information

Entry
Database: PDB / ID: 6kdy
TitleCrystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.
Components(Isocitrate dehydrogenase [NAD] subunit ...) x 2
KeywordsOXIDOREDUCTASE / NAD dependent isocitrate dehydrogenase
Function / homology
Function and homology information


: / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity ...: / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / magnesium ion binding / mitochondrion / nucleus
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL / Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsSun, P. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular basis for the function of the alpha beta heterodimer of human NAD-dependent isocitrate dehydrogenase.
Authors: Sun, P. / Ma, T. / Zhang, T. / Zhu, H. / Zhang, J. / Liu, Y. / Ding, J.
History
DepositionJul 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
C: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,20117
Polymers306,1208
Non-polymers4,0819
Water00
1
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3884
Polymers76,5302
Non-polymers8582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-34 kcal/mol
Surface area25160 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8025
Polymers76,5302
Non-polymers1,2723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-35 kcal/mol
Surface area24910 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5364
Polymers76,5302
Non-polymers1,0062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-43 kcal/mol
Surface area24400 Å2
MethodPISA
4
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4764
Polymers76,5302
Non-polymers9462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-33 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.460, 162.979, 114.407
Angle α, β, γ (deg.)90.000, 100.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Isocitrate dehydrogenase [NAD] subunit ... , 2 types, 8 molecules ACEGBDFH

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


Mass: 36826.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3A / Production host: Escherichia coli (E. coli)
References: UniProt: P50213, isocitrate dehydrogenase (NAD+)
#2: Protein
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / Isocitric dehydrogenase subunit beta / NAD(+)-specific ICDH subunit beta


Mass: 39703.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3B / Production host: Escherichia coli (E. coli) / References: UniProt: O43837

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Non-polymers , 5 types, 9 molecules

#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Chemical ChemComp-PE7 / 1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL


Mass: 342.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7S
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM

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Details

Has ligand of interestY
Sequence detailsTHIS SEQUENCE OF IDH3 B CORRESPONDS TO THE A ISOFORM FOUND IN UNP O43837.

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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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05M ICT, 0.05M NAD, 0.2 M calcium acetate (pH 7.5) and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.001→50 Å / Num. obs: 71108 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.051 / Rrim(I) all: 0.095 / Χ2: 1.062 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.02-3.133.40.50571040.7850.3230.6010.60599.9
3.13-3.253.50.35270370.8810.220.4160.542100
3.25-3.43.50.25971190.9260.1640.3070.619100
3.4-3.583.30.16871050.9620.110.2020.80199.8
3.58-3.83.50.13170730.9770.0820.1551.03399.9
3.8-4.13.40.171150.9840.0630.1181.27799.9
4.1-4.513.30.07370910.9910.0470.0871.51399.9
4.51-5.163.40.05871400.9940.0360.0681.63999.9
5.16-6.53.40.05371240.9950.0340.0631.41399.7
6.5-503.20.02872000.9990.0180.0331.22299.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDE

6kde


Resolution: 3.02→48.928 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.44
RfactorNum. reflection% reflection
Rfree0.2459 3598 5.06 %
Rwork0.1971 --
obs0.1995 71060 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 243.45 Å2 / Biso mean: 71.4049 Å2 / Biso min: 26.83 Å2
Refinement stepCycle: final / Resolution: 3.02→48.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19885 0 271 0 20156
Biso mean--79.37 --
Num. residues----2697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.02-3.04060.404990.3356216884
3.0406-3.08220.36441410.29872634100
3.0822-3.12620.33351780.26742562100
3.1262-3.17290.30251170.25482628100
3.1729-3.22250.28671610.25522579100
3.2225-3.27530.33011470.25772596100
3.2753-3.33180.34071430.25922610100
3.3318-3.39230.29611220.24172600100
3.3923-3.45760.27411500.23382622100
3.4576-3.52810.3361410.23322590100
3.5281-3.60480.26831370.22472602100
3.6048-3.68860.28481410.21682630100
3.6886-3.78080.24321280.20932582100
3.7808-3.8830.23961380.2072630100
3.883-3.99720.23181440.19352620100
3.9972-4.12620.22891360.18872598100
4.1262-4.27360.22911320.17832606100
4.2736-4.44460.21031370.16872637100
4.4446-4.64670.19671500.15742583100
4.6467-4.89150.19881180.16252616100
4.8915-5.19760.20961470.15972636100
5.1976-5.59840.21871400.18882609100
5.5984-6.16080.22811390.18822632100
6.1608-7.05010.21211450.17122625100
7.0501-8.87370.2131180.16642655100
8.8737-48.9280.24291490.1841261298

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