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- PDB-2dht: Crystal structure of isocitrate dehydrogenase from Sulfolobus tok... -

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Basic information

Entry
Database: PDB / ID: 2dht
TitleCrystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7
Components409aa long hypothetical NADP-dependent isocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / homo dimer
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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKondo, H. / Murakami, M. / Ihara, K. / Suzuki, S. / Kouyama, T.
CitationJournal: To be Published
Title: Crystal structure of isocitrate dehydrogenase of Sulfolobus tokodaii strain7
Authors: Kondo, H. / Murakami, M. / Ihara, K. / Suzuki, S. / Kouyama, T.
History
DepositionMar 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 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

Downloads & links

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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
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-38 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.979, 88.095, 76.216
Angle α, β, γ (deg.)90.00, 91.32, 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 (archaea) / Strain: str. 7 / Production host: Escherichia coli (E. coli)
References: GenBank: 15623283, UniProt: Q96YK6*PLUS, isocitrate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
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: BL41XU / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 30, 2005
RadiationMonochromator: double-crystal monochomator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→53.6 Å / Num. all: 33797 / Num. obs: 33300 / % possible obs: 97.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 3.2 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4511 / Rsym value: 0.492 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
XTALVIEWrefinement
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1v94

1v94


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1474 4.4 %RANDOM
Rwork0.241 ---
obs0.241 31055 98.5 %-
all-31851 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 39.5232 Å2 / ksol: 0.333597 e/Å3
Displacement parametersBiso max: 121.83 Å2 / Biso mean: 55.96 Å2 / Biso min: 20.26 Å2
Baniso -1Baniso -2Baniso -3
1-11.98 Å20 Å23.15 Å2
2---15.6 Å20 Å2
3---3.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.49 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 0 38 6484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.378190.50.36940910.0874168411098.6
2.61-2.750.33721050.3339650.0234245417598.4
2.75-2.920.352285.50.30239190.0234211414798.5
2.92-3.140.3222205.30.28639210.0224203414198.5
3.14-3.460.3071814.40.26939520.0234216413398
3.46-3.950.2791994.80.25439550.024222415498.4
3.95-4.950.2582054.90.20339980.0184258420398.7
4.95-150.21421250.18740250.0154304423798.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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