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- PDB-6kde: Crystal structure of the alpha beta heterodimer of human IDH3 in ... -

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Basic information

Entry
Database: PDB / ID: 6kde
TitleCrystal structure of the alpha beta heterodimer of human IDH3 in complex with Ca(2+)
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
KeywordsOXIDOREDUCTASE / NAD dependent isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate dehydrogenase complex (NAD+) / 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 complex (NAD+) / 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
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: 2.999 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 2, 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 ...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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,1406
Polymers153,0604
Non-polymers802
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)76,5703
Polymers76,5302
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-42 kcal/mol
Surface area24500 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)76,5703
Polymers76,5302
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-43 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.200, 166.200, 128.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 36826.305 Da / Num. of mol.: 2
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.: 2
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M 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: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.999→50 Å / Num. obs: 34725 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.073 / Χ2: 0.531 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.60.50434640.8360.2970.5890.42699.4
3.11-3.233.70.36834330.90.2120.4270.44199.6
3.23-3.383.90.25934810.9460.1440.2980.45299.7
3.38-3.563.90.17734750.9730.10.2050.48999.5
3.56-3.783.90.11234460.9880.0640.130.49899.3
3.78-4.073.70.08234520.9920.0480.0960.5499.1
4.07-4.483.80.05834920.9960.0330.0670.57599.7
4.48-5.1340.04535020.9970.0260.0520.59699.7
5.13-6.463.70.04734710.9970.0270.0540.57299.2
6.46-503.80.03235090.9990.0180.0370.71298.3

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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: 5GRH

5grh


Resolution: 2.999→41.367 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.243 1706 4.92 %
Rwork0.1942 --
obs0.1965 34690 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.39 Å2 / Biso mean: 75.1623 Å2 / Biso min: 40.21 Å2
Refinement stepCycle: final / Resolution: 2.999→41.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9630 0 2 0 9632
Biso mean--70.14 --
Num. residues----1304
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9992-3.08740.31361650.2484270299
3.0874-3.1870.3411470.24992768100
3.187-3.30090.29111110.25232749100
3.3009-3.4330.35311070.24812794100
3.433-3.58910.23731180.22672756100
3.5891-3.77820.25651280.2031274499
3.7782-4.01480.27041510.1977273199
4.0148-4.32450.22721810.17272728100
4.3245-4.75910.21531540.15052762100
4.7591-5.44640.23451760.16942705100
5.4464-6.85680.23521300.2061277399
6.8568-41.3670.20461380.1809277297

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