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- PDB-1iyz: Crystal Structures of the Quinone Oxidoreductase from Thermus the... -

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Basic information

Entry
Database: PDB / ID: 1iyz
TitleCrystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH
ComponentsQUINONE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / PROTEIN-NADPH COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


NADPH:quinone reductase / quinone reductase (NADPH) activity / nucleotide binding
Similarity search - Function
: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Probable quinone oxidoreductase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsShimomura, Y. / Kakuta, Y. / Fukuyama, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Bacteriol. / Year: 2003
Title: Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH: Implication for NADPH and Substrate Recognition
Authors: Shimomura, Y. / Kakuta, Y. / Fukuyama, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Overproduction, crystallization and preliminary X-ray diffraction analysis of a quinone oxidoreductase from Thermus thermophilus HB8
Authors: Shimomura, Y. / Sumiguchi-Agari, K. / Masui, R. / Kuramitsu, S. / Fukuyama, K.
History
DepositionSep 17, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: QUINONE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8722
Polymers32,1271
Non-polymers7451
Water64936
1
A: QUINONE OXIDOREDUCTASE
hetero molecules

A: QUINONE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7444
Polymers64,2532
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-5/61
Unit cell
Length a, b, c (Å)77.633, 77.633, 235.614
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein QUINONE OXIDOREDUCTASE


Mass: 32126.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8L3C8, NADPH:quinone reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.31 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: ammonium dihydrogen phosphate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8 / Method: vapor diffusion, hanging drop
Details: Shimomura, Y., (2002) Acta Crystallogr.,Sect.D, 58, 1365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.4 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
41 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 278044 / Num. obs: 278044 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.5 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 11091 / Num. measured all: 278044 / Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.205

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→44.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 532329.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1109 10.2 %RANDOM
Rwork0.219 ---
all0.2235 10881 --
obs0.2235 10881 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.738 Å2 / ksol: 0.37952 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å28.33 Å20 Å2
2--4.61 Å20 Å2
3----9.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 48 36 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d3.71
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 169 10 %
Rwork0.283 1529 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NDP_XPLOR.PARAMNDP_XPLOR.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.7

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