[English] 日本語
Yorodumi
- PDB-7zxv: Orange Carotenoid Protein Trp-288 BTA mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zxv
TitleOrange Carotenoid Protein Trp-288 BTA mutant
ComponentsOrange carotenoid-binding protein
KeywordsPLANT PROTEIN / Orange Carotenoid Protein / photoconversion / non-canonical amino acids / 3-benzothienyl-L-alanine
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-carotene-4,4'-dione / beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMoldenhauer, M. / Tseng, H.-W. / Kraskov, A. / Tavraz, N.N. / Hildebrandt, P. / Hochberg, G. / Essen, L.-O. / Budisa, N. / Korf, L. / Maksimov, E.G. / Friedrich, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN764591European Union
CitationJournal: Front Mol Biosci / Year: 2023
Title: Parameterization of a single H-bond in Orange Carotenoid Protein by atomic mutation reveals principles of evolutionary design of complex chemical photosystems.
Authors: Moldenhauer, M. / Tseng, H.W. / Kraskov, A. / Tavraz, N.N. / Yaroshevich, I.A. / Hildebrandt, P. / Sluchanko, N.N. / Hochberg, G.A. / Essen, L.O. / Budisa, N. / Korf, L. / Maksimov, E.G. / Friedrich, T.
History
DepositionMay 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Feb 7, 2024Group: Refinement description / Category: 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)35,8534
Polymers34,7021
Non-polymers1,1513
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.195, 83.195, 88.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

-
Components

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 34701.656 Da / Num. of mol.: 1 / Mutation: W288BTA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1963 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74102
#2: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone / Echinenone


Mass: 550.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin / Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M MgCl2, 0.1 M Tris pH=7.0, 10 %(w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→72.05 Å / Num. obs: 32925 / % possible obs: 98.7 % / Redundancy: 20.2 % / Biso Wilson estimate: 37.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.037 / Rrim(I) all: 0.12 / Χ2: 0.99 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 20.1 % / Rmerge(I) obs: 4.998 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1940 / CC1/2: 0.477 / Rpim(I) all: 1.628 / Rrim(I) all: 5.574 / Χ2: 0.91 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5tuw

5tuw


Resolution: 1.8→55.91 Å / SU ML: 0.2871 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 1640 4.99 %
Rwork0.173 31224 -
obs0.1753 32864 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 84 307 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122608
X-RAY DIFFRACTIONf_angle_d1.07863565
X-RAY DIFFRACTIONf_chiral_restr0.0642390
X-RAY DIFFRACTIONf_plane_restr0.0098481
X-RAY DIFFRACTIONf_dihedral_angle_d15.953976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.5271290.44762587X-RAY DIFFRACTION99.31
1.85-1.910.33271510.31912574X-RAY DIFFRACTION99.89
1.91-1.980.30011360.24762613X-RAY DIFFRACTION99.85
1.98-2.060.25871390.20332613X-RAY DIFFRACTION99.96
2.06-2.150.23391590.2092579X-RAY DIFFRACTION100
2.15-2.270.25011250.19642186X-RAY DIFFRACTION83.88
2.27-2.410.24531230.17732629X-RAY DIFFRACTION99.96
2.41-2.60.24561270.16342664X-RAY DIFFRACTION100
2.6-2.860.22891330.18952645X-RAY DIFFRACTION99.96
2.86-3.270.21681320.17942656X-RAY DIFFRACTION100
3.27-4.120.20691240.15962689X-RAY DIFFRACTION100
4.12-55.910.18941620.13892789X-RAY DIFFRACTION100
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)
12.6936473809-0.2045852032230.06881497922440.7797249544580.1594953622531.38834899188-0.103096794865-0.2490580891270.0858612883084-0.02046859202260.0446747173612-0.06256742765290.009382374752990.249761074693-3.09455341602E-50.2718290013830.03029269428660.01498499324710.322743242969-0.004850005337730.29273243324623.947702570410.5496491373-4.06104104105
21.04865318806-0.242977206042-0.1031986414920.222422044193-0.4049601801711.41095436872-0.238858121859-0.1750155823250.692271994088-0.09333796143340.004742333497330.413854588511-0.1785062028470.147794720345-0.01845424534090.3230719354650.0301533348592-0.0186235928620.359651590182-0.02871525374630.42381110592619.906467974116.0464862993-6.48005169902
32.65575066497-0.3235815948130.8694576252552.26948306336-0.3384446262552.48178404911-0.1560115626910.1928075057970.0841579122453-0.2038705419920.04294229394780.128664850094-0.1174880699320.114047769335-2.74573632419E-50.360718842321-0.0499023504797-0.04686502404510.2755760364870.02034449458420.27819204111211.55628224919.4338099312-24.4942849508
40.1394272066560.05143913322350.05924923781220.08919989438950.05021364261990.119974501361-0.25863808047-0.1585435941740.162155878196-0.0234838820032-0.0265027292167-0.0890439466869-0.314827646399-0.00669567184283-0.002597667832920.2602829670280.03612054512290.07627419674660.2827777753250.03991658487930.31746816607220.52334440711.481919534-12.8024960536
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 146 )A2 - 1461 - 145
22chain 'A' and (resid 147 through 169 )A147 - 169146 - 168
33chain 'A' and (resid 170 through 314 )A - C170 - 314169 - 313
44chain 'A' and (resid 401 through 402 )D - E401 - 402

+
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