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- PDB-4f8y: Complex structure of NADPH:quinone oxidoreductase with menadione ... -

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Basic information

Entry
Database: PDB / ID: 4f8y
TitleComplex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans
ComponentsNADPH Quinone Oxidoreductase
KeywordsOXIDOREDUCTASE / NADPH / Quinone Oxidoreductase / FAD
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / MENADIONE / Oxidoreductase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsWang, Z. / Li, L. / Su, X.-D.
CitationJournal: TO BE PUBLISHED
Title: Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans
Authors: Wang, Z. / Li, L. / Su, X.-D.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: NADPH Quinone Oxidoreductase
B: NADPH Quinone Oxidoreductase
C: NADPH Quinone Oxidoreductase
D: NADPH Quinone Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,14512
Polymers91,3144
Non-polymers3,8318
Water10,052558
1
A: NADPH Quinone Oxidoreductase
B: NADPH Quinone Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5726
Polymers45,6572
Non-polymers1,9154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-24 kcal/mol
Surface area15890 Å2
MethodPISA
2
C: NADPH Quinone Oxidoreductase
D: NADPH Quinone Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5726
Polymers45,6572
Non-polymers1,9154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-26 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.614, 79.413, 106.502
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADPH Quinone Oxidoreductase


Mass: 22828.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU_1420 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DTD1, NAD(P)H dehydrogenase (quinone)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-VK3 / MENADIONE / VITAMIN K3 / 2-METHYL-1,4-NAPHTHALENEDIONE


Mass: 172.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES pH7.5, 35% v/v Pentaerythritol propoxylate(5/4 PO/OH), EVAPORATION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. all: 78361 / Num. obs: 77264 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→19.959 Å / σ(F): 1.35 / Phase error: 18.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 3925 5.08 %random
Rwork0.1556 ---
obs0.157 77239 98.18 %-
all-78361 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.566 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5748 Å2-0 Å21.4719 Å2
2---1.1081 Å2-0 Å2
3---0.5333 Å2
Refinement stepCycle: LAST / Resolution: 1.796→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 264 558 6966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066603
X-RAY DIFFRACTIONf_angle_d1.0849039
X-RAY DIFFRACTIONf_dihedral_angle_d18.292431
X-RAY DIFFRACTIONf_chiral_restr0.068985
X-RAY DIFFRACTIONf_plane_restr0.0061092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.796-1.82660.29081610.27062953X-RAY DIFFRACTION98
1.8266-1.85980.32871760.26463480X-RAY DIFFRACTION98
1.8598-1.89550.29451810.26063593X-RAY DIFFRACTION98
1.8955-1.93420.26631930.24553697X-RAY DIFFRACTION98
1.9342-1.97620.25522050.23423698X-RAY DIFFRACTION98
1.9762-2.02210.24491900.22463719X-RAY DIFFRACTION98
2.0221-2.07260.24452170.21383681X-RAY DIFFRACTION98
2.0726-2.12860.20951800.20343749X-RAY DIFFRACTION98
2.1286-2.19120.222030.19093753X-RAY DIFFRACTION98
2.1912-2.26180.21912080.18883700X-RAY DIFFRACTION98
2.2618-2.34250.21112030.18423702X-RAY DIFFRACTION98
2.3425-2.43610.21212070.17983712X-RAY DIFFRACTION98
2.4361-2.54680.19332150.17383734X-RAY DIFFRACTION98
2.5468-2.68080.19492030.16823746X-RAY DIFFRACTION98
2.6808-2.84830.18351950.1553716X-RAY DIFFRACTION98
2.8483-3.06750.18071940.14573722X-RAY DIFFRACTION98
3.0675-3.37490.14621940.11663756X-RAY DIFFRACTION98
3.3749-3.86010.13051830.09543701X-RAY DIFFRACTION98
3.8601-4.85180.09452000.08013704X-RAY DIFFRACTION98
4.8518-19.9590.16311890.13283826X-RAY DIFFRACTION98

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