[English] 日本語
Yorodumi
- PDB-8srl: Crystal structure of T151V CAO1 in complex with piceatannol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8srl
TitleCrystal structure of T151V CAO1 in complex with piceatannol
ComponentsCarotenoid oxygenase
KeywordsOXIDOREDUCTASE / non-heme iron / beta propeller / stilbene / mutant
Function / homologyCarotenoid 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 / BENZOIC ACID / : / PICEATANNOL / Carotenoid oxygenase
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 Å
AuthorsKiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2107713 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Spectroscopy and crystallography define carotenoid oxygenases as a new subclass of mononuclear non-heme Fe II enzymes.
Authors: DeWeese, D.E. / Everett, M.P. / Babicz Jr., J.T. / Daruwalla, A. / Solomon, E.I. / Kiser, P.D.
History
DepositionMay 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2May 7, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carotenoid oxygenase
B: Carotenoid oxygenase
C: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,67316
Polymers237,9844
Non-polymers1,68912
Water36,0482001
1
A: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8368
Polymers118,9922
Non-polymers8446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase
C: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8368
Polymers118,9922
Non-polymers8446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.888, 100.888, 448.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
Carotenoid oxygenase


Mass: 59495.965 Da / Num. of mol.: 4 / Mutation: T151V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: GE21DRAFT_6499 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0DIC8
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL


Mass: 244.243 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2001 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 42% sodium polyacrylate 2100 0.05 M HEPES-NaOH pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→50.13 Å / Num. obs: 177907 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Net I/σ(I): 12.77
Reflection shellResolution: 2.01→2.13 Å / Rmerge(I) obs: 2.377 / Num. unique obs: 28339 / CC1/2: 0.413 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.01→50.13 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.846 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19136 7766 4.4 %RANDOM
Rwork0.16749 ---
obs0.16857 170141 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.01→50.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15942 0 112 2001 18055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01216846
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615216
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.65222938
X-RAY DIFFRACTIONr_angle_other_deg0.3721.57435128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34552044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.79.685254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0310.6862603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.73515119
X-RAY DIFFRACTIONr_chiral_restr0.0530.22311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024123
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3013.9698101
X-RAY DIFFRACTIONr_mcbond_other2.3013.9698101
X-RAY DIFFRACTIONr_mcangle_it3.3447.12410170
X-RAY DIFFRACTIONr_mcangle_other3.3467.12410171
X-RAY DIFFRACTIONr_scbond_it3.234.3398745
X-RAY DIFFRACTIONr_scbond_other3.234.3398746
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1357.812769
X-RAY DIFFRACTIONr_long_range_B_refined7.14947.3119470
X-RAY DIFFRACTIONr_long_range_B_other7.13547.2319427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.059 Å
RfactorNum. reflection% reflection
Rfree0.331 624 -
Rwork0.342 12296 -
obs--99.35 %

+
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