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- PDB-3jyl: Crystal structures of Pseudomonas syringae pv. Tomato DC3000 quin... -

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Basic information

Entry
Database: PDB / ID: 3jyl
TitleCrystal structures of Pseudomonas syringae pv. Tomato DC3000 quinone oxidoreductase
ComponentsQuinone oxidoreductase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


NADPH:quinone reductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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
Quinone oxidoreductase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPan, X. / Zhang, H. / Gao, Y. / Li, M. / Chang, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structures of Pseudomonas syringae pv. tomato DC3000 quinone oxidoreductase and its complex with NADPH
Authors: Pan, X. / Zhang, H. / Gao, Y. / Li, M. / Chang, W.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Quinone oxidoreductase


Theoretical massNumber of molelcules
Total (without water)34,3781
Polymers34,3781
Non-polymers00
Water4,558253
1
A: Quinone oxidoreductase

A: Quinone oxidoreductase


Theoretical massNumber of molelcules
Total (without water)68,7562
Polymers68,7562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2140 Å2
ΔGint-11 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.560, 63.560, 130.149
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Quinone oxidoreductase


Mass: 34378.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88B47, NADPH:quinone reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCl(pH 8.5), 0.2M MgCl2, 30%PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 9, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→23.24 Å / Num. all: 12435 / Num. obs: 12429 / % possible obs: 99.95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1204 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOR

1qor


Resolution: 2.4→23.24 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24862 636 5.1 %RANDOM
Rwork0.20215 ---
all0.205 11799 --
obs0.2044 11793 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0.38 Å20 Å2
2---0.76 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→23.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 0 253 2675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_bond_d0.0076
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 57 -
Rwork0.243 818 -
obs-1204 100 %

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