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- PDB-5j53: The Structure and Mechanism of NOV1, a Resveratrol-Cleaving Dioxy... -

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Basic information

Entry
Database: PDB / ID: 5j53
TitleThe Structure and Mechanism of NOV1, a Resveratrol-Cleaving Dioxygenase
ComponentsCarotenoid oxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / Resveratrol / Stilbene / Carotenoid / beta-propeller / metalloprotein
Function / homologyOxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding / : / OXYGEN MOLECULE / TRIETHYLENE GLYCOL / Dioxygenase
Function and homology information
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 / Category: database_2 / pdbx_audit_support
Item: _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)55,7224
Polymers55,4841
Non-polymers2383
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.422, 101.338, 144.521
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-1084-

HOH

21A-1131-

HOH

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Components

#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
#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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 535 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
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: SSRL / Beamline: BL12-2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 87570 / % possible obs: 93.2 % / Redundancy: 7 % / Biso Wilson estimate: 22.3280153507 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.8
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.988 / Mean I/σ(I) obs: 1.35 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIXdev_2276refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIW

2biw


Resolution: 1.61→42.72 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 0.1224 / Phase error: 20.39
RfactorNum. reflection% reflection
Rfree0.1782 1757 2.29 %
Rwork0.1498 --
obs0.1505 76791 87.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.06 Å2
Refinement stepCycle: LAST / Resolution: 1.61→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 13 535 4355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0100064534093951
X-RAY DIFFRACTIONf_angle_d0.9950112473275351
X-RAY DIFFRACTIONf_chiral_restr0.062749818896549
X-RAY DIFFRACTIONf_plane_restr0.00754561181737711
X-RAY DIFFRACTIONf_dihedral_angle_d14.6451388792313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6104-1.6540.351040.3144587X-RAY DIFFRACTION70.57
1.654-1.70260.3141200.294919X-RAY DIFFRACTION75.22
1.7026-1.75760.3091230.2625126X-RAY DIFFRACTION78.56
1.7576-1.82040.2361320.2255269X-RAY DIFFRACTION80.58
1.8204-1.89330.271270.1945389X-RAY DIFFRACTION82.46
1.8933-1.97950.2411190.1765577X-RAY DIFFRACTION84.86
1.9795-2.08380.1831370.1565972X-RAY DIFFRACTION91.12
2.0838-2.21440.1891430.1426082X-RAY DIFFRACTION92.33
2.2144-2.38530.1791400.1426099X-RAY DIFFRACTION92.88
2.3853-2.62530.1691460.1456248X-RAY DIFFRACTION94.71
2.6253-3.00520.191520.1436367X-RAY DIFFRACTION96.09
3.0052-3.78580.151540.1326552X-RAY DIFFRACTION98.37
3.7858-42.740.1421600.1276847X-RAY DIFFRACTION99.34
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)
12.77439902688-1.811233540372.385376878525.24624437365-4.836005491015.90865612327-0.02995334858850.0009409533884520.1929770056730.3627621879790.09992232303270.299227793007-0.394907016983-0.149257076541-0.0510254624960.2047136519630.02846233975410.0395067334490.221348912173-0.04891545852180.18591863688319.997552909254.166308700864.6422669432
20.702523384006-0.1081505134170.0005559498350632.69931492731-1.020845436291.990615426310.004301110430060.001449424142670.03566958845270.0266410433340.0301204030455-0.0885699349243-0.08679950506530.0478236967993-0.09873774151760.12294464802-0.005200187326660.008023513025210.167406389544-0.005469063533410.15816688668929.540614487548.791892747156.9520447939
31.10791034782-0.08666293089730.4678254747111.119252663910.1303816877361.604960070120.002321490166590.139262461145-0.0737482993637-0.2286950022650.0218909027272-0.2504764581290.01339465734620.285120100582-0.05072306370280.220762802790.01727803945580.06307731693450.263593811926-0.01469589906690.24880368070335.398098097141.380548574142.9274524649
40.8540851951610.5526129083240.1064026990151.950164495440.5906365610831.67842085993-0.002471068762510.219760259623-0.059462835964-0.275884427982-0.000330652625716-0.0825243216709-0.09532811854180.132916005406-0.009169581141280.2043118859660.02891380828830.0329813471720.209931948567-0.0221292558940.17415975103425.630303945938.197474759434.9422715368
51.25361871914-0.308928607543-0.4140233538753.086932989790.6921332411961.386148096550.05875937668670.0697192142790.162842966094-0.119899068834-0.07688593690820.450671913245-0.122321362854-0.2491680406160.1021899988510.2029122989590.0606765484006-0.01630313476540.256312532838-0.03864392419150.27704465347510.071832256441.321209311240.32790466
61.30982233253-0.239500640999-0.3412118122681.959075350491.402759501183.34916573440.02603994358050.051363136026-0.110357147717-0.0328783489747-0.1357076830740.1224777629560.169420721074-0.2199214078380.07582298460920.21338992045-0.01328383608490.008685625719830.183120008692-0.02337676024520.23565908665816.807092569126.953372401842.9286641279
76.20540273666-2.12121266679-1.239925600384.443640861671.428107465514.33706436747-0.03341248814920.05975431746790.1006814215230.0248584167164-0.1118740979450.4211158005290.135194697834-0.7259216538450.120263342070.179175635325-0.08517213114190.02668844648270.323902857091-0.02180123505920.2361670698326.6187870928631.24421705555.7217848
82.19659104602-0.6867886319-0.1445582093926.055731781331.780284927023.34751161340.0437243563378-0.202424999026-0.1674112517830.274139780247-0.0697583786597-0.02473209016170.39740877387-0.2256808884590.03050770946580.211977729837-0.0603620611080.02855133014510.1849635988340.03144315612840.14465327325117.370904402329.784982179761.4180558776
91.607044639180.2910413209220.03817499482294.14624437806-0.145788804952.653787875690.0131987912709-0.173394917024-0.1044836337670.280923562633-0.05889966785160.1353295688890.194048218197-0.1296515524740.04101351148670.208569059037-0.02532797492480.01668201644710.1971877796410.007015003435850.13771401572620.383846342236.1328983165.4412123713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 148 )
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 190 )
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 325 )
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 373 )
7X-RAY DIFFRACTION7chain 'A' and (resid 374 through 404 )
8X-RAY DIFFRACTION8chain 'A' and (resid 405 through 441 )
9X-RAY DIFFRACTION9chain 'A' and (resid 442 through 488 )

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