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- PDB-6ixt: Crystal structure of isocitrate dehydrogenase from Ostreococcus t... -

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Basic information

Entry
Database: PDB / ID: 6ixt
TitleCrystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with NAD+ and Mg2+
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / isocitrate dehydrogenase NAD+
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Isocitrate dehydrogenase (NAD(+)), mitochondrial / Isocitrate dehydrogenase (NAD(+)), mitochondrial
Similarity search - Component
Biological speciesOstreococcus tauri (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _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
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)189,78319
Polymers187,2954
Non-polymers2,48815
Water20,3391129
1
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,90410
Polymers93,6472
Non-polymers1,2568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-95 kcal/mol
Surface area31450 Å2
MethodPISA
2
C: Isocitrate dehydrogenase
D: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8799
Polymers93,6472
Non-polymers1,2327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-96 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.392, 79.178, 112.097
Angle α, β, γ (deg.)90.27, 102.33, 112.52
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


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

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Non-polymers , 5 types, 1144 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / 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: 56.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 18% PEG8000, 0.1M (NH4)2SO4, and 0.1M 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: 0.979305 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979305 Å / Relative weight: 1
ReflectionResolution: 1.78→20 Å / Num. obs: 184833 / % possible obs: 93.7 % / Redundancy: 2.4 % / Net I/σ(I): 13.1
Reflection shellResolution: 1.78→1.87 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.654 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112
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
Rfree0.21638 9201 5 %RANDOM
Rwork0.19042 ---
obs0.19172 175609 93.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.15 Å20.17 Å2
2--0.13 Å20.22 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.78→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12602 0 119 1129 13850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912980
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212122
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.94817599
X-RAY DIFFRACTIONr_angle_other_deg0.926327781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84851616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04723.355611
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.823152119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.82415109
X-RAY DIFFRACTIONr_chiral_restr0.0780.21948
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023044
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_it0.9091.7236476
X-RAY DIFFRACTIONr_mcbond_other0.9091.7236475
X-RAY DIFFRACTIONr_mcangle_it1.5052.588088
X-RAY DIFFRACTIONr_mcangle_other1.5052.588089
X-RAY DIFFRACTIONr_scbond_it1.1651.8546504
X-RAY DIFFRACTIONr_scbond_other1.1541.8426472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8882.719464
X-RAY DIFFRACTIONr_long_range_B_refined3.89614.14415537
X-RAY DIFFRACTIONr_long_range_B_other3.613.81114990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.778→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 669 -
Rwork0.256 12341 -
obs--90.09 %

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