[English] 日本語
Yorodumi
- PDB-8a0h: Crystal structure of the E25A mutant of the Orange Carotenoid Pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a0h
TitleCrystal structure of the E25A mutant of the Orange Carotenoid Protein X from Gloeobacter kilaueensis JS1 complexed with echinenone
ComponentsOCP N-terminal domain-containing protein
KeywordsTRANSPORT PROTEIN / carotenoid-binding protein / carotenoid transport / CBP / Gloeobacter kilaueensis / nuclear transport factor 2
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding
Similarity search - Function
Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / NTF2-like domain superfamily
Similarity search - Domain/homology
beta,beta-caroten-4-one / OCP N-terminal domain-containing protein
Similarity search - Component
Biological speciesGloeobacter kilaueensis JS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsBoyko, K.M. / Slonimskiy, Y.B. / Zupnik, A.O. / Varfolomeeva, L.A. / Maksimov, E.G. / Sluchanko, N.N.
Funding support Russian Federation, Germany, 3items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Foundation for Basic Research20-54-12018 Russian Federation
German Research Foundation (DFG)FR1276/6-1 Germany
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: A primordial Orange Carotenoid Protein: Structure, photoswitching activity and evolutionary aspects.
Authors: Slonimskiy, Y.B. / Zupnik, A.O. / Varfolomeeva, L.A. / Boyko, K.M. / Maksimov, E.G. / Sluchanko, N.N.
History
DepositionMay 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: 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: OCP N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5614
Polymers35,8181
Non-polymers7433
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.735, 61.366, 145.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein OCP N-terminal domain-containing protein


Mass: 35817.793 Da / Num. of mol.: 1 / Mutation: E25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter kilaueensis JS1 (bacteria) / Gene: GKIL_2275 / Production host: Escherichia coli (E. coli) / References: UniProt: U5QHX0
#2: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.73→72.54 Å / Num. obs: 35299 / % possible obs: 97.9 % / Redundancy: 4.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Rrim(I) all: 0.102 / Net I/σ(I): 10.3 / Num. measured all: 144313 / Scaling rejects: 123
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.73-1.760.361668718120.8390.2160.4253.592.7
8.99-72.540.04110282810.9920.0250.04821.889.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
MOLREPphasing
REFMAC5.8.0350refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 1.73→72.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.022 / SU ML: 0.066 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 1799 5.1 %RANDOM
Rwork0.1577 ---
obs0.1595 33412 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.1 Å2 / Biso mean: 14.25 Å2 / Biso min: 3.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å2-0 Å2
2---0.07 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.73→72.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 51 404 2934
Biso mean--19.62 24.23 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122625
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162403
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.6413582
X-RAY DIFFRACTIONr_angle_other_deg0.7711.5455584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.3237.22236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98110395
X-RAY DIFFRACTIONr_chiral_restr0.1120.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023062
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02522
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 121 -
Rwork0.204 2372 -
all-2493 -
obs--95.15 %

+
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