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- PDB-6ixl: Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri -

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Basic information

Entry
Database: PDB / ID: 6ixl
TitleCrystal structure of isocitrate dehydrogenase from Ostreococcus tauri
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) activity / NAD metabolic process / tricarboxylic acid cycle / magnesium ion binding / protein homodimerization activity / mitochondrion
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
Isocitrate dehydrogenase (NAD(+)), mitochondrial / Isocitrate dehydrogenase (NAD(+)), mitochondrial
Similarity search - Component
Biological speciesOstreococcus tauri (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZhu, G.P. / Tang, W.G. / Wang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570010 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
DepositionDec 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: 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 1.2Mar 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

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Assembly

Deposited unit
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
C: Isocitrate dehydrogenase
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,32815
Polymers187,2954
Non-polymers1,03311
Water18,3211017
1
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2128
Polymers93,6472
Non-polymers5646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-81 kcal/mol
Surface area31280 Å2
MethodPISA
2
C: Isocitrate dehydrogenase
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1167
Polymers93,6472
Non-polymers4685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-59 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.517, 79.273, 112.014
Angle α, β, γ (deg.)90.26, 102.32, 112.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Isocitrate dehydrogenase /


Mass: 46823.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostreococcus tauri (plant) / Gene: BE221DRAFT_192402 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y5IEA9, UniProt: A0A096P8D3*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1017 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 22% PEG8000, 0.1 M (NH4)2SO4 and 0.1 M MES (pH 6.5)

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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: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 199682 / % possible obs: 96.4 % / Redundancy: 2.9 % / Net I/σ(I): 13.9
Reflection shellResolution: 1.75→1.84 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.435 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20977 9913 5 %RANDOM
Rwork0.18361 ---
obs0.18491 189769 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.31 Å20.25 Å2
2--0.35 Å2-0.33 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12587 0 61 1017 13665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912929
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212116
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.94217517
X-RAY DIFFRACTIONr_angle_other_deg0.923327775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83951621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22323.431612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.556152125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.64915107
X-RAY DIFFRACTIONr_chiral_restr0.0790.21940
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214729
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9791.8826478
X-RAY DIFFRACTIONr_mcbond_other0.9781.8826477
X-RAY DIFFRACTIONr_mcangle_it1.5662.8178092
X-RAY DIFFRACTIONr_mcangle_other1.5662.8178093
X-RAY DIFFRACTIONr_scbond_it1.3322.0216451
X-RAY DIFFRACTIONr_scbond_other1.3252.0146431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1252.9599393
X-RAY DIFFRACTIONr_long_range_B_refined3.70315.23915307
X-RAY DIFFRACTIONr_long_range_B_other3.49714.95614806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 702 -
Rwork0.278 13806 -
obs--95.44 %

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