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- PDB-5vn0: Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) boun... -

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Basic information

Entry
Database: PDB / ID: 5vn0
TitleWater-forming NADH oxidase from Lactobacillus brevis (LbNOX) bound to NADH.
ComponentsNAD(FAD)-dependent dehydrogenase
KeywordsOXIDOREDUCTASE / Substrate bound / redox active cysteine / water-forming oxidase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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 ...: / 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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / Uncharacterized NAD(FAD)-dependent dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsCracan, V. / Grabarek, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM099683 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: A genetically encoded tool for manipulation of NADP(+)/NADPH in living cells.
Authors: Cracan, V. / Titov, D.V. / Shen, H. / Grabarek, Z. / Mootha, V.K.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: NAD(FAD)-dependent dehydrogenase
B: NAD(FAD)-dependent dehydrogenase
C: NAD(FAD)-dependent dehydrogenase
D: NAD(FAD)-dependent dehydrogenase
E: NAD(FAD)-dependent dehydrogenase
F: NAD(FAD)-dependent dehydrogenase
G: NAD(FAD)-dependent dehydrogenase
H: NAD(FAD)-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,70145
Polymers449,0308
Non-polymers12,67137
Water46,5332583
1
A: NAD(FAD)-dependent dehydrogenase
B: NAD(FAD)-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,41011
Polymers112,2572
Non-polymers3,1529
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-56 kcal/mol
Surface area32090 Å2
MethodPISA
2
C: NAD(FAD)-dependent dehydrogenase
D: NAD(FAD)-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,41011
Polymers112,2572
Non-polymers3,1529
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12180 Å2
ΔGint-53 kcal/mol
Surface area32230 Å2
MethodPISA
3
E: NAD(FAD)-dependent dehydrogenase
F: NAD(FAD)-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,47212
Polymers112,2572
Non-polymers3,21410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-55 kcal/mol
Surface area31930 Å2
MethodPISA
4
G: NAD(FAD)-dependent dehydrogenase
H: NAD(FAD)-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,41011
Polymers112,2572
Non-polymers3,1529
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-57 kcal/mol
Surface area31990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.525, 107.511, 119.298
Angle α, β, γ (deg.)63.370, 90.040, 89.950
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
NAD(FAD)-dependent dehydrogenase


Mass: 56128.723 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (strain ATCC 367 / JCM 1170) (bacteria)
Strain: ATCC 367 / JCM 1170 / Gene: LVIS_1558 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q03Q85

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Non-polymers , 5 types, 2620 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2583 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop
Details: Crystalls were grown in 20% PEG 3350, 0.2M NH4Cl, soaked briefly for 1-3 min in the formulation with 20-30mM NADH and quickly frozen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97007 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2016
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97007 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 282997 / % possible obs: 98.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.85 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.062 / Rrim(I) all: 0.121 / Χ2: 0.983 / Net I/σ(I): 6 / Num. measured all: 1096258
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.70.735139680.8170.440.8570.66796.8
2.03-2.073.80.649140330.8670.3850.7550.69197
2.07-2.113.80.538139270.8940.3180.6260.69897
2.11-2.153.90.489140580.9120.2890.5680.71197.1
2.15-2.23.90.449140640.9350.2640.5210.72997.2
2.2-2.253.90.385140410.9490.2270.4470.76397.3
2.25-2.313.90.351139630.960.2060.4080.8197.5
2.31-2.373.90.317141260.9610.1870.3680.78397.7
2.37-2.443.90.262141330.9740.1540.3040.80697.9
2.44-2.523.90.233141710.9710.1370.2710.84498
2.52-2.613.90.188141300.9860.110.2180.84198.1
2.61-2.713.90.166141550.9870.0970.1920.92598.2
2.71-2.843.90.141143330.990.0820.1630.98198.4
2.84-2.993.90.118141080.9930.0690.1361.10198.5
2.99-3.173.90.095141920.9950.0560.111.21498.6
3.17-3.423.90.078142890.9950.0460.0911.41998.9
3.42-3.763.90.063142440.9960.0370.0731.52399
3.76-4.313.80.053143270.9970.0310.0611.5999.2
4.31-5.433.80.043143770.9980.0260.051.42399.4
5.43-5040.031143580.9990.0180.0361.08899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ER0

5er0


Resolution: 2.001→42.948 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 14404 5.1 %
Rwork0.1795 267937 -
obs0.1818 282341 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.55 Å2 / Biso mean: 29.2999 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: final / Resolution: 2.001→42.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27418 0 1378 2583 31379
Biso mean--26.46 33.5 -
Num. residues----3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00628817
X-RAY DIFFRACTIONf_angle_d0.83739335
X-RAY DIFFRACTIONf_chiral_restr0.0524575
X-RAY DIFFRACTIONf_plane_restr0.0055004
X-RAY DIFFRACTIONf_dihedral_angle_d13.57717012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0008-2.02360.35364020.30968155855788
2.0236-2.04740.3584590.29768877933697
2.0474-2.07240.31534710.27478847931897
2.0724-2.09860.28034660.26448930939697
2.0986-2.12620.2985140.24718759927397
2.1262-2.15530.33044970.25118827932497
2.1553-2.18610.29474600.24658970943097
2.1861-2.21870.26764640.23248821928597
2.2187-2.25340.26994290.22129034946397
2.2534-2.29040.2554050.2119001940697
2.2904-2.32980.28064920.22168829932197
2.3298-2.37220.27335120.2078867937998
2.3722-2.41780.2725140.21048886940098
2.4178-2.46720.22934490.19388988943798
2.4672-2.52080.2334620.19538992945498
2.5208-2.57950.25415800.18658862944298
2.5795-2.6440.25744540.18719026948098
2.644-2.71540.27555030.1948929943298
2.7154-2.79530.22865780.18498911948998
2.7953-2.88550.26455000.19098977947798
2.8855-2.98860.24114440.18569067951198
2.9886-3.10830.22135450.17558957950298
3.1083-3.24970.21854400.17469057949798
3.2497-3.42090.23595440.17848954949899
3.4209-3.63520.1985290.16029015954499
3.6352-3.91570.20374690.1569081955099
3.9157-4.30940.15634390.13299109954899
4.3094-4.93220.15764190.12259187960699
4.9322-6.2110.18025010.14259096959799
6.211-42.95740.13344630.12698926938997

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