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- PDB-4la4: Crystal structure of native PnpB -

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Basic information

Entry
Database: PDB / ID: 4la4
TitleCrystal structure of native PnpB
ComponentsNAD(P)H dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / native PnpB / para-benzoquinone reductase
Function / homology
Function and homology information


p-benzoquinone reductase (NADPH) / p-benzoquinone reductase (NADPH) activity / 4-nitrophenol catabolic process / NAD(P)H dehydrogenase (quinone) activity / generation of precursor metabolites and energy / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding / membrane
Similarity search - Function
NAD(P)H dehydrogenase (quinone), prokaryotic / Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
p-benzoquinone reductase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSu, J. / Zhang, C. / Li, N. / Gu, L.
CitationJournal: To be Published
Title: Crystal structure of native PnpB
Authors: Su, J. / Zhang, C. / Li, N. / Gu, L.
History
DepositionJun 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)


Theoretical massNumber of molelcules
Total (without water)44,1222
Polymers44,1222
Non-polymers00
Water1,802100
1
A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)

A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)


Theoretical massNumber of molelcules
Total (without water)88,2444
Polymers88,2444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area11710 Å2
ΔGint-67 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.145, 73.110, 84.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-32-

ASP

21A-303-

HOH

31A-326-

HOH

41A-341-

HOH

51A-342-

HOH

61B-301-

HOH

71B-312-

HOH

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Components

#1: Protein NAD(P)H dehydrogenase (quinone) / NAD(P)H:quinone oxidoreductase


Mass: 22061.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: WBC-3 / Gene: pnpB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C1I202, NAD(P)H dehydrogenase (quinone)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 22471 / Num. obs: 22471 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 %
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.07-2.145.50.3145.142081194
4.46-506.90.05334.392431199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→40.116 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.868 / SU ML: 0.2 / σ(F): 0 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1937 8.89 %RANDOM
Rwork0.1756 ---
all0.1786 21778 --
obs0.1786 21778 95.69 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.024 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 31.8854 Å2 / Biso min: 14.95 Å2
Baniso -1Baniso -2Baniso -3
1-10.5593 Å2-0 Å2-0 Å2
2---7.202 Å20 Å2
3----3.3573 Å2
Refinement stepCycle: LAST / Resolution: 2.07→40.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 0 100 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083006
X-RAY DIFFRACTIONf_angle_d1.0084074
X-RAY DIFFRACTIONf_dihedral_angle_d15.0191080
X-RAY DIFFRACTIONf_chiral_restr0.071462
X-RAY DIFFRACTIONf_plane_restr0.004528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0685-2.12030.23161130.17091175128881
2.1203-2.17760.23871280.18211327145590
2.1776-2.24160.22431300.1711319144991
2.2416-2.3140.20391310.17581354148594
2.314-2.39670.22631330.17961419155296
2.3967-2.49260.22081380.16861393153196
2.4926-2.60610.23691420.16891429157197
2.6061-2.74340.24371400.17081432157298
2.7434-2.91530.20661440.18341452159698
2.9153-3.14030.24881410.18091455159699
3.1403-3.45610.20791460.17021476162299
3.4561-3.95590.19561450.177214941639100
3.9559-4.98250.18041490.159115161665100
4.9825-40.12340.19871570.194716001757100

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