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- PDB-5j55: The Structure and Mechanism of NOV1, a Resveratrol-Cleaving Dioxy... -

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Basic information

Entry
Database: PDB / ID: 5j55
TitleThe Structure and Mechanism of NOV1, a Resveratrol-Cleaving Dioxygenase
ComponentsCarotenoid oxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / Resveratrol / Stilbene / Carotenoid / beta-propeller / metalloprotein
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
: / OXYGEN MOLECULE / TRIETHYLENE GLYCOL / 4-hydroxy-3-methoxybenzaldehyde / Dioxygenase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMcAndrew, R.P. / Pereira, J.H. / Sathitsuksanoh, N. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Department of Energy (DOE, United States)DE-FG02-07ER64495 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase.
Authors: McAndrew, R.P. / Sathitsuksanoh, N. / Mbughuni, M.M. / Heins, R.A. / Pereira, J.H. / George, A. / Sale, K.L. / Fox, B.G. / Simmons, B.A. / Adams, P.D.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8755
Polymers55,4841
Non-polymers3904
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.246, 101.122, 144.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1044-

HOH

21A-1091-

HOH

31A-1139-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carotenoid oxygenase /


Mass: 55484.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain DSM 12444 / F199) (bacteria)
Strain: DSM 12444 / F199 / Gene: Saro_0802 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2GA76

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Non-polymers , 5 types, 546 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin / Vanillin


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M MgCl2, 0.08 M Tris pH 8.5, 18% (w/v) PEG 4000, and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 68233 / % possible obs: 93.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.5427222283 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.44 / % possible all: 53.2

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Processing

Software
NameVersionClassification
PHENIXdev_2276refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J53

5j53


Resolution: 1.75→49.58 Å / SU ML: 0.145 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.679
RfactorNum. reflection% reflection
Rfree0.1665 1998 3.13 %
Rwork0.1401 --
obs0.1409 63823 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 24 542 4381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00998934791033970
X-RAY DIFFRACTIONf_angle_d0.9748207634075376
X-RAY DIFFRACTIONf_chiral_restr0.0595820916535551
X-RAY DIFFRACTIONf_plane_restr0.00732450001347713
X-RAY DIFFRACTIONf_dihedral_angle_d14.78702510312320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7484-1.79210.272810.222480X-RAY DIFFRACTION53.2
1.7921-1.84060.2251080.23362X-RAY DIFFRACTION71.22
1.8406-1.89470.191290.183993X-RAY DIFFRACTION85.71
1.8947-1.95590.2051440.194459X-RAY DIFFRACTION94.72
1.9559-2.02580.1821510.154674X-RAY DIFFRACTION99.46
2.0258-2.10690.1851510.154697X-RAY DIFFRACTION99.87
2.1069-2.20280.1561530.134713X-RAY DIFFRACTION100
2.2028-2.31890.1651520.144728X-RAY DIFFRACTION99.96
2.3189-2.46420.1711510.134672X-RAY DIFFRACTION100
2.4642-2.65440.1871540.144733X-RAY DIFFRACTION100
2.6544-2.92150.1711540.144768X-RAY DIFFRACTION99.98
2.9215-3.34420.1551540.134774X-RAY DIFFRACTION100
3.3442-4.2130.1451550.124803X-RAY DIFFRACTION99.88
4.213-49.60850.1541610.144969X-RAY DIFFRACTION99.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.749285818178-0.083672111799-0.04614371751251.97010395261-0.5436780253341.841231127880.0171046522636-0.04040828230970.05066295647570.05989518900920.00113965244267-0.0580081668955-0.1283129500290.00430113217128-0.01557630552750.100576110007-0.003083852118070.0083852127480.129975031613-0.006386317672130.13529106936927.889689819349.590751740158.3381294482
21.30749847495-0.2140979145530.8217695667331.3879814064-0.466354091632.753653981830.02243883190170.147637926581-0.0521369542099-0.262679253043-0.00758746501399-0.2831858457760.00701045212060.286849454825-0.02209375886520.1202622935480.02178146136640.06689586513510.17761406862-0.01854487837080.18309986742935.368082733741.261655450643.008636407
30.9728032834130.5526626992450.0930430811272.066050662650.5311406557941.699040039890.006597370570680.174129389319-0.0591099450005-0.282321524363-0.0129498424156-0.0911015680246-0.1038558499260.1073438452980.005360924156240.1758454581850.02867925332690.03821362667420.165957745766-0.02029884139560.13272767381325.578569737338.111534955935.0640273226
41.90436807196-1.78733197767-0.1455441518247.008559315160.1544920047730.5157497430080.1026512426590.09501848812190.0570742559224-0.191596214403-0.1427589595490.519332154234-0.0961897048046-0.2330304652090.04354568806550.1640259987360.0559061777955-0.02356249343390.206191629498-0.04744633230060.18303171011310.056661095241.229336587240.5523587634
51.494738065350.0840977016785-0.08127845046431.835633839871.318971745694.095846992080.04491587135940.00609383902402-0.0865381174471-0.0243307425994-0.1324392267990.1074699155570.21325232602-0.1973868060310.07973466928350.138293547014-0.01570858981020.005692660687480.0949018169979-0.02082835974730.16043451186516.767168655426.843375244143.0692742292
66.21564282703-2.99999919304-1.189372650768.346263940132.189063544584.367484502010.01670065632770.02118546721020.0758374321753-0.125626606833-0.2549210450550.344000260660.0682617364798-0.7319639371120.1641695690480.137451802833-0.09196751677940.01636006119360.309459691157-0.04386975446310.1848426546416.5864971825731.489944001755.7172451091
71.679199236120.163783334698-0.156235249623.911701222510.8754910324162.965189886670.075600074447-0.143267506836-0.1827250815090.338481175981-0.146687004177-0.01700643781120.454852275947-0.2335441241470.04669854344150.191690774012-0.06092735410070.01817952106140.1545582378240.01008445102440.14303021659217.36515995629.617022665461.5405241596
81.527938873930.616675605182-0.02038589940313.07504562612-0.01936859658522.322760732580.0398016788432-0.142079795928-0.1119794816670.302141067443-0.06038028122240.1217157690520.198078636705-0.1743286126070.01365808096910.172489783615-0.03319011676720.01819240318190.1530695810360.005353728387650.106118186820.371589221735.96538050365.554933393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 293 )
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 325 )
5X-RAY DIFFRACTION5chain 'A' and (resid 326 through 373 )
6X-RAY DIFFRACTION6chain 'A' and (resid 374 through 404 )
7X-RAY DIFFRACTION7chain 'A' and (resid 405 through 441 )
8X-RAY DIFFRACTION8chain 'A' and (resid 442 through 488 )

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