[English] 日本語
Yorodumi
- PDB-8ov5: PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ov5
TitlePERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K
ComponentsPeridinin-chlorophyll a-binding protein 1, chloroplastic
KeywordsPHOTOSYNTHESIS / Light Harvesting / Carotenoid / Chlorophyll / Lipid / Dinoflagellates
Function / homology
Function and homology information


light-harvesting complex / chlorophyll binding / chloroplast
Similarity search - Function
Peridinin-chlorophyll A binding protein / Peridinin-chlorophyll A binding superfamily / Peridinin-chlorophyll A binding protein
Similarity search - Domain/homology
CHLOROPHYLL A / PERIDININ / : / Peridinin-chlorophyll a-binding protein 1, chloroplastic
Similarity search - Component
Biological speciesAmphidinium carterae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsHofmann, E. / Johanning, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB480 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP).
Authors: Schulte, T. / Magdaong, N.C.M. / Di Valentin, M. / Agostini, A. / Tait, C.E. / Niedzwiedzki, D.M. / Carbonera, D. / Hofmann, E.
History
DepositionApr 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Oct 16, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: Peridinin-chlorophyll a-binding protein 1, chloroplastic
N: Peridinin-chlorophyll a-binding protein 1, chloroplastic
O: Peridinin-chlorophyll a-binding protein 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,40142
Polymers97,5633
Non-polymers26,83839
Water32,2831792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50970 Å2
ΔGint-264 kcal/mol
Surface area33990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.140, 115.610, 65.880
Angle α, β, γ (deg.)90.000, 94.970, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11N-845-

HOH

21N-968-

HOH

31N-1084-

HOH

41N-1087-

HOH

51N-1261-

HOH

-
Components

-
Protein , 1 types, 3 molecules MNO

#1: Protein Peridinin-chlorophyll a-binding protein 1, chloroplastic / PCP


Mass: 32521.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphidinium carterae (eukaryote) / Production host: Amphidinium carterae (eukaryote) / References: UniProt: P80484

-
Non-polymers , 5 types, 1831 molecules

#2: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-PID / PERIDININ


Mass: 630.810 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C39H50O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-W4I / [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-[(6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoyl]oxy-propyl] (5~{Z},8~{Z},11~{Z},14~{Z},17~{Z})-icosa-5,8,11,14,17-pentaenoate


Mass: 959.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C53H82O15 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1792 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 14% PEG8000, 100mM Tris-HCL pH 7.5, 200mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.15→49.82 Å / Num. obs: 444109 / % possible obs: 85.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.05 / Net I/σ(I): 13.33
Reflection shellResolution: 1.15→1.18 Å / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 12493 / CC1/2: 0.44 / Rrim(I) all: 1.111 / % possible all: 32.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
XSCALEVERSION Feb 5, 2021 BUILT=20210323data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.15→43.38 Å / SU ML: 0.0938 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1547 22204 5 %
Rwork0.1407 421860 -
obs0.1414 444064 85.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.41 Å2
Refinement stepCycle: LAST / Resolution: 1.15→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 1908 1792 10546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01229639
X-RAY DIFFRACTIONf_angle_d1.180913398
X-RAY DIFFRACTIONf_chiral_restr0.07191371
X-RAY DIFFRACTIONf_plane_restr0.01491740
X-RAY DIFFRACTIONf_dihedral_angle_d21.03773570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.33622530.31814798X-RAY DIFFRACTION29.36
1.16-1.180.2772980.29265658X-RAY DIFFRACTION34.35
1.18-1.190.29853490.28276632X-RAY DIFFRACTION40.5
1.19-1.210.28153960.27767540X-RAY DIFFRACTION46.16
1.21-1.220.27594470.26098488X-RAY DIFFRACTION51.74
1.22-1.240.26415040.24329594X-RAY DIFFRACTION58.39
1.24-1.260.25495610.227310678X-RAY DIFFRACTION65.18
1.26-1.280.24816230.226111809X-RAY DIFFRACTION72.22
1.28-1.30.24126970.215713242X-RAY DIFFRACTION80.56
1.3-1.320.21627880.205214959X-RAY DIFFRACTION90.99
1.32-1.340.20518630.192316390X-RAY DIFFRACTION99.95
1.34-1.360.19168600.178316323X-RAY DIFFRACTION99.95
1.36-1.390.18818610.173116410X-RAY DIFFRACTION99.79
1.39-1.420.19218620.164916375X-RAY DIFFRACTION99.92
1.42-1.450.17448640.155416423X-RAY DIFFRACTION99.83
1.45-1.480.15788610.144716368X-RAY DIFFRACTION99.83
1.48-1.520.1558620.133516369X-RAY DIFFRACTION99.9
1.52-1.560.1448650.128916434X-RAY DIFFRACTION99.87
1.56-1.610.14868650.12716433X-RAY DIFFRACTION99.97
1.61-1.660.14358630.121716400X-RAY DIFFRACTION99.94
1.66-1.720.13648610.123116363X-RAY DIFFRACTION99.95
1.72-1.790.14528670.125816459X-RAY DIFFRACTION99.96
1.79-1.870.13978660.127116465X-RAY DIFFRACTION99.98
1.87-1.970.14378620.129916374X-RAY DIFFRACTION99.86
1.97-2.090.13768650.129516431X-RAY DIFFRACTION99.86
2.09-2.250.13468650.122916441X-RAY DIFFRACTION99.93
2.25-2.480.12998670.116416450X-RAY DIFFRACTION99.79
2.48-2.840.13728670.126316483X-RAY DIFFRACTION99.76
2.84-3.570.1518690.138616478X-RAY DIFFRACTION99.78
3.57-43.380.15318730.139916593X-RAY DIFFRACTION99.47

+
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