[English] 日本語
Yorodumi
- PDB-6t6m: Y201W mutant of the orange carotenoid protein from Synechocystis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t6m
TitleY201W mutant of the orange carotenoid protein from Synechocystis at pH 5.5
ComponentsOrange carotenoid-binding protein
KeywordsPLANT PROTEIN / orange carotenoid protein / photoactive protein / mutant
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity
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 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily
Similarity search - Domain/homology
beta,beta-caroten-4-one / HISTIDINE / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSluchanko, N.N. / Gushchin, I. / Botnarevskiy, V.S. / Slonimskiy, Y.B. / Remeeva, A. / Kovalev, K. / Stepanov, A.V. / Gordeliy, V. / Maksimov, E.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00691 Russian Federation
CitationJournal: Commun Biol / Year: 2021
Title: Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein.
Authors: Yaroshevich, I.A. / Maksimov, E.G. / Sluchanko, N.N. / Zlenko, D.V. / Stepanov, A.V. / Slutskaya, E.A. / Slonimskiy, Y.B. / Botnarevskii, V.S. / Remeeva, A. / Gushchin, I. / Kovalev, K. / ...Authors: Yaroshevich, I.A. / Maksimov, E.G. / Sluchanko, N.N. / Zlenko, D.V. / Stepanov, A.V. / Slutskaya, E.A. / Slonimskiy, Y.B. / Botnarevskii, V.S. / Remeeva, A. / Gushchin, I. / Kovalev, K. / Gordeliy, V.I. / Shelaev, I.V. / Gostev, F.E. / Khakhulin, D. / Poddubnyy, V.V. / Gostev, T.S. / Cherepanov, D.A. / Polivka, T. / Kloz, M. / Friedrich, T. / Paschenko, V.Z. / Nadtochenko, V.A. / Rubin, A.B. / Kirpichnikov, M.P.
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2544
Polymers36,4551
Non-polymers7993
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.149, 83.149, 87.488
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-680-

HOH

-
Components

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 36454.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Tyr201 is mutated to Trp in Synechocystis OCP. / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: Synechocystis sp. PCC 6803 / Gene: slr1963 / Production host: Escherichia coli (E. coli) / References: UniProt: P74102
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1 M Sodium citrate pH5.5 20 % w/v PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.49→41.61 Å / Num. obs: 57478 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 37.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
1.49-1.5220.21.2383.328070.88100
8.16-41.5713.80.0363900.99197.4

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XB5

4xb5


Resolution: 1.49→41.6 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 2.768 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.058
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1672 2826 4.9 %RANDOM
Rwork0.1284 ---
obs0.1303 54626 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 192.88 Å2 / Biso mean: 32.465 Å2 / Biso min: 20.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: final / Resolution: 1.49→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 57 337 2749
Biso mean--34.17 47.32 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132561
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172408
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.6463506
X-RAY DIFFRACTIONr_angle_other_deg1.3831.5685581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98521.361147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9181514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_rigid_bond_restr14.10134968
LS refinement shellResolution: 1.49→1.529 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 216 -
Rwork0.183 3956 -
all-4172 -
obs--99.98 %
Refinement TLS params.

T23: 0 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0210.0091-0.00180.014-0.0040.0072-0.0015-0.0010.0004-0.00070.00120.00210.0019-0.00040.00040.00060.0001-00.00030.0228-22.2354-7.7713-15.0559
200000000000000-00.008000.0080.008000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 1301
2X-RAY DIFFRACTION2A0

+
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://pdbjlvh1.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