[English] 日本語
Yorodumi
- PDB-5j55: The Structure and Mechanism of NOV1, a Resveratrol-Cleaving Dioxy... -

+
Open data


ID or keywords:

Loading...

-
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


carotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 546 molecules

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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more