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- PDB-4laf: Crystal structure of PnpB complex with FMN -

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Basic information

Entry
Database: PDB / ID: 4laf
TitleCrystal structure of PnpB complex with FMN
ComponentsNAD(P)H dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / para-benzoquinone reductase / PnpB in complex with FMN
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
FLAVIN MONONUCLEOTIDE / p-benzoquinone reductase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsSu, J. / Zhang, C. / Li, N. / Gu, L.
CitationJournal: To be Published
Title: Crystal structure of PnpB complex with FMN
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 / 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: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
C: NAD(P)H dehydrogenase (quinone)
D: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0698
Polymers88,2444
Non-polymers1,8254
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15290 Å2
ΔGint-106 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.553, 188.553, 61.203
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 22061.021 Da / Num. of mol.: 4
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: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES monohydrate pH6.0, 20% Polyethylene glycol monomethyl ether 2000, 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: Jun 10, 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: 1.76→50 Å / Num. all: 80299 / Num. obs: 80299 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 16.83 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.76-1.8250.3185.6379671100
3.79-505.60.05228.248026199.8

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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: 1.761→35.633 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8687 / SU ML: 0.2 / σ(F): 0.08 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1909 2.48 %RANDOM
Rwork0.191 ---
all0.1915 76906 --
obs0.1915 76906 95.75 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.979 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 79.57 Å2 / Biso mean: 20.086 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.5811 Å20 Å20 Å2
2---0.5811 Å2-0 Å2
3---1.1621 Å2
Refinement stepCycle: LAST / Resolution: 1.761→35.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 124 0 6040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066175
X-RAY DIFFRACTIONf_angle_d1.0318392
X-RAY DIFFRACTIONf_dihedral_angle_d16.3252230
X-RAY DIFFRACTIONf_chiral_restr0.066935
X-RAY DIFFRACTIONf_plane_restr0.0061071
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 (%)
1.7607-1.80480.28091330.21375116524992
1.8048-1.85360.25691290.20425276540594
1.8536-1.90810.21521200.20914862498287
1.9081-1.96970.2841330.20925047518091
1.9697-2.04010.18491400.18085365550596
2.0401-2.12180.23431320.19185283541594
2.1218-2.21830.25291380.19465423556197
2.2183-2.33520.23611380.21275315545395
2.3352-2.48150.22531440.19585517566198
2.4815-2.67310.18751390.19865517565699
2.6731-2.94190.24651420.21575534567699
2.9419-3.36740.22651430.20155835726100
3.3674-4.24140.16511380.177355765714100
4.2414-35.64040.17851400.160655835723100

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