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- PDB-5er0: Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) -

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Basic information

Entry
Database: PDB / ID: 5er0
TitleWater-forming NADH oxidase from Lactobacillus brevis (LbNOX)
ComponentsNADH oxidase
KeywordsOXIDOREDUCTASE / NADH oxidase / FAD / molecular oxygen
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / NADH oxidase / Uncharacterized NAD(FAD)-dependent dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsCracan, V. / Grabarek, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099683 United States
CitationJournal: Science / Year: 2016
Title: Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio.
Authors: Titov, D.V. / Cracan, V. / Goodman, R.P. / Peng, J. / Grabarek, Z. / Mootha, V.K.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: NADH oxidase
B: NADH oxidase
C: NADH oxidase
D: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,53024
Polymers224,5154
Non-polymers4,01520
Water17,042946
1
A: NADH oxidase
B: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,32713
Polymers112,2572
Non-polymers2,07011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-36 kcal/mol
Surface area34740 Å2
MethodPISA
2
C: NADH oxidase
D: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,20311
Polymers112,2572
Non-polymers1,9459
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-37 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.968, 86.350, 93.327
Angle α, β, γ (deg.)96.920, 94.070, 92.400
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NADH oxidase


Mass: 56128.723 Da / Num. of mol.: 4 / Fragment: UNP residues 19-468
Source method: isolated from a genetically manipulated source
Details: N-terminal His6 tag residues: 1-50 LbNOX coding sequence residues: 51-500 C-terminal FLAG tag residues: 501-518
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: M5B0V2, UniProt: Q03Q85*PLUS
#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 946 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 10 mg/ml protein in 10 mM HEPES, pH 7.5, 100 mM NaCl mixed 1:1 (v/v) with well solution (30 % PEG 3350, 0.2 M NH4Cl).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2014
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 79832 / % possible obs: 98.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.12 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.066 / Rrim(I) all: 0.13 / Χ2: 0.816 / Net I/av σ(I): 10.632 / Net I/σ(I): 5.2 / Num. measured all: 310221
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.50.432.139260.8580.2640.5050.48996.6
2.44-2.493.70.42739550.8790.2550.4980.54697.8
2.49-2.533.80.39639760.8750.2340.4610.63898
2.53-2.593.90.34539460.9250.2020.40.51798
2.59-2.643.90.33940030.9210.1980.3930.53998.1
2.64-2.73.90.33239800.5540.1930.3851.00198.2
2.7-2.773.90.2539650.9550.1460.290.56198.4
2.77-2.853.90.23239590.9170.1360.2690.5998.2
2.85-2.933.90.19840160.9720.1150.2290.57398.5
2.93-3.023.90.16639330.9810.0970.1920.5998.5
3.02-3.133.90.12640230.9880.0730.1460.6398.7
3.13-3.263.90.12239880.9660.0710.1420.75798.7
3.26-3.413.90.09739820.9920.0570.1130.72298.8
3.41-3.583.90.09740570.9850.0570.1131.09599
3.58-3.813.90.08939830.9720.0520.1041.17899
3.81-4.13.90.07640340.9890.0450.0891.12399.2
4.1-4.523.90.06240170.9940.0360.0721.12299.3
4.52-5.173.80.05940210.9950.0350.0691.01799.4
5.17-6.513.80.06740280.9930.040.0780.84499.6
6.51-5040.04540400.9970.0260.0521.69399.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CDU

2cdu


Resolution: 2.406→48.029 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 4044 5.07 %Random selection
Rwork0.1723 75738 --
obs0.1745 79782 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.1 Å2 / Biso mean: 28.6607 Å2 / Biso min: 8.53 Å2
Refinement stepCycle: final / Resolution: 2.406→48.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13736 0 268 947 14951
Biso mean--24.21 30.97 -
Num. residues----1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214260
X-RAY DIFFRACTIONf_angle_d0.46319424
X-RAY DIFFRACTIONf_chiral_restr0.0432260
X-RAY DIFFRACTIONf_plane_restr0.0042496
X-RAY DIFFRACTIONf_dihedral_angle_d11.4918532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4064-2.43470.27871040.2252187229181
2.4347-2.46440.28551280.21582571269998
2.4644-2.49560.2831310.21192648277998
2.4956-2.52840.26881070.212655276298
2.5284-2.56310.27771250.2082573269898
2.5631-2.59970.27011410.20212653279498
2.5997-2.63850.26271270.20832592271998
2.6385-2.67970.28221280.20822639276798
2.6797-2.72360.25011670.20032615278298
2.7236-2.77060.25661370.19812595273298
2.7706-2.8210.28341390.20122638277798
2.821-2.87520.2491430.1932610275398
2.8752-2.93390.24361350.18912646278198
2.9339-2.99770.24291470.1842608275598
2.9977-3.06740.22931160.18352643275998
3.0674-3.14410.22341260.17922614274099
3.1441-3.22910.22971510.18512656280799
3.2291-3.32410.23171420.1842621276399
3.3241-3.43140.23521550.17142592274799
3.4314-3.5540.19191420.16542656279899
3.554-3.69620.1991380.16612632277099
3.6962-3.86440.19911430.1582649279299
3.8644-4.0680.20941590.15452598275799
4.068-4.32270.16621480.13662669281799
4.3227-4.65620.15481480.13252622277099
4.6562-5.12430.18461410.14292651279299
5.1243-5.86470.18731680.16926412809100
5.8647-7.38460.20781360.174526442780100
7.3846-48.03820.17361720.14452620279299

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