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- PDB-7e2w: Crystal structure of isocitrate dehydrogenase from Ostreococcus t... -

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Basic information

Entry
Database: PDB / ID: 7e2w
TitleCrystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with isocitrate and magnesium(II)
ComponentsIsocitrate dehydrogenase (NAD(+)), mitochondrial
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / NAD metabolic process / tricarboxylic acid cycle / peroxisome / magnesium ion binding / protein homodimerization activity ...isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / NAD metabolic process / tricarboxylic acid cycle / peroxisome / magnesium ion binding / protein homodimerization activity / mitochondrion / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
CITRATE ANION / ISOCITRIC ACID / ISOPROPYL ALCOHOL / Isocitrate dehydrogenase (NAD(+)), mitochondrial
Similarity search - Component
Biological speciesOstreococcus tauri (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsZhu, G.P. / Tang, W.G. / Wang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570010 China
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Crystal structures of NAD + -linked isocitrate dehydrogenase from the green alga Ostreococcus tauri and its evolutionary relationship with eukaryotic NADP + -linked homologs.
Authors: Tang, W. / Wu, M. / Qin, N. / Liu, L. / Meng, R. / Wang, C. / Wang, P. / Zang, J. / Zhu, G.
History
DepositionFeb 7, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 19, 2021ID: 6IXU
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 29, 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(+)), mitochondrial
B: Isocitrate dehydrogenase (NAD(+)), mitochondrial
C: Isocitrate dehydrogenase (NAD(+)), mitochondrial
D: Isocitrate dehydrogenase (NAD(+)), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,15713
Polymers187,2954
Non-polymers8629
Water12,484693
1
A: Isocitrate dehydrogenase (NAD(+)), mitochondrial
B: Isocitrate dehydrogenase (NAD(+)), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1136
Polymers93,6472
Non-polymers4664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-38 kcal/mol
Surface area30540 Å2
MethodPISA
2
C: Isocitrate dehydrogenase (NAD(+)), mitochondrial
D: Isocitrate dehydrogenase (NAD(+)), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0447
Polymers93,6472
Non-polymers3965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-28 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 78.511, 111.056
Angle α, β, γ (deg.)89.150, 103.590, 111.890
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrate dehydrogenase (NAD(+)), mitochondrial / OtIDH


Mass: 46823.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostreococcus tauri (plant) / Gene: IDH, Ot_13g02940, BE221DRAFT_192402 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A096P8D3, isocitrate dehydrogenase (NAD+)

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Non-polymers , 6 types, 702 molecules

#2: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 4000, 10% 2-propanol, 0.1 M sodium citrate (pH 5.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 177015 / % possible obs: 94.9 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 26019 / CC1/2: 0.84

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IXL

6ixl


Resolution: 1.8→19.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.355 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 8824 5 %RANDOM
Rwork0.208 ---
obs0.2095 168180 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.09 Å2 / Biso mean: 29.875 Å2 / Biso min: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.56 Å21.74 Å2
2---0.46 Å20.24 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.8→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12288 0 57 693 13038
Biso mean--39.79 34.54 -
Num. residues----1603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312600
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711663
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.64717081
X-RAY DIFFRACTIONr_angle_other_deg1.5631.58126737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58551597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47121.588655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21152000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5121591
X-RAY DIFFRACTIONr_chiral_restr0.0910.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022914
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 687 -
Rwork0.299 12514 -
all-13201 -
obs--95.27 %

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