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- PDB-1x0l: Crystal structure of tetrameric homoisocitrate dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 1x0l
TitleCrystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus
ComponentsHomoisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / DECARBOXYLATING DEHYDROGENASE / Lysine biosynthesis
Function / homology
Function and homology information


isocitrate-homoisocitrate dehydrogenase / homoisocitrate dehydrogenase activity / isocitrate dehydrogenase (NAD+) activity / lysine biosynthetic process via aminoadipic acid / isocitrate metabolic process / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
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/homoisocitrate dehydrogenase / Isocitrate/homoisocitrate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMiyazaki, J. / Asada, K. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal Structure of Tetrameric Homoisocitrate Dehydrogenase from an Extreme Thermophile, Thermus thermophilus: Involvement of Hydrophobic Dimer-Dimer Interaction in Extremely High Thermotolerance
Authors: Miyazaki, J. / Asada, K. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
History
DepositionMar 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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: Homoisocitrate dehydrogenase
B: Homoisocitrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)71,6722
Polymers71,6722
Non-polymers00
Water6,810378
1
A: Homoisocitrate dehydrogenase
B: Homoisocitrate dehydrogenase

A: Homoisocitrate dehydrogenase
B: Homoisocitrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)143,3454
Polymers143,3454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9290 Å2
ΔGint-71 kcal/mol
Surface area49860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.963, 143.243, 177.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: x, -y, -z

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Components

#1: Protein Homoisocitrate dehydrogenase


Mass: 35836.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: hicdh / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codonplus RIL
References: UniProt: Q8RQU4, UniProt: Q72IW9*PLUS, homoisocitrate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.71 Å3/Da / Density % sol: 54.56 %

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Redundancy: 4.1 % / Biso Wilson estimate: 16.7 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3039919.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3357 5 %RANDOM
Rwork0.216 ---
obs-66504 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1355 Å2 / ksol: 0.367834 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20 Å2
2--5.23 Å20 Å2
3----3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 0 378 5361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.461.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it4.012
X-RAY DIFFRACTIONc_scangle_it5.552.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 562 5.2 %
Rwork0.234 10219 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3CIS_PEPTIDE11.PARAM

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