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- PDB-2e0c: crystal structure of isocitrate dehydrogenase from Sulfolobus tok... -

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Basic information

Entry
Database: PDB / ID: 2e0c
Titlecrystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 at 2.0 A resolution
Components409aa long hypothetical NADP-dependent isocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / homedimer
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / tricarboxylic acid cycle / nucleotide binding / metal ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
isocitrate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKouyama, T.
CitationJournal: Archaea / Year: 2018
Title: Crystal Structures of the Putative Isocitrate Dehydrogenase fromSulfolobus tokodaiiStrain 7 in the Apo and NADP+-Bound Forms.
Authors: Kondo, H. / Murakami, M.
History
DepositionOct 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Oct 25, 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: 409aa long hypothetical NADP-dependent isocitrate dehydrogenase
B: 409aa long hypothetical NADP-dependent isocitrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)93,1182
Polymers93,1182
Non-polymers00
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-34 kcal/mol
Surface area32130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.880, 87.720, 75.720
Angle α, β, γ (deg.)90.00, 91.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 409aa long hypothetical NADP-dependent isocitrate dehydrogenase / isocitrate dehydrogenase


Mass: 46558.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: strain 7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96YK6, isocitrate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 66041 / Num. obs: 65823 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9631 / Rsym value: 0.413 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dht

2dht


Resolution: 2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 3320 -RANDOM
Rwork0.2214 ---
all0.2214 66041 --
obs0.2473 65537 99.2 %-
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.957 Å20 Å20 Å2
2--2.543 Å20 Å2
3----1.586 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6418 0 0 463 6881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_deg1.264
X-RAY DIFFRACTIONc_dihedral_angle_d22.07
X-RAY DIFFRACTIONc_improper_angle_d0.832

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