[English] 日本語
Yorodumi
- PDB-1ppr: PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ppr
TitlePERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE
ComponentsPERIDININ-CHLOROPHYLL PROTEIN
KeywordsLIGHT-HARVESTING PROTEIN / LIGHT HARVESTING PROTEIN / PHOTOSYNTHESIS / CAROTENOIDS / DINOFLAGELLATES
Function / homology
Function and homology information


light-harvesting complex / chlorophyll binding / chloroplast
Similarity search - Function
Peridinin-chlorophyll Protein, Chain M / Peridinin-chlorophyll A binding / Peridinin-chlorophyll A binding protein / Peridinin-chlorophyll A binding superfamily / Peridinin-chlorophyll A binding protein / Alpha solenoid / Mainly Alpha
Similarity search - Domain/homology
CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / PERIDININ / Peridinin-chlorophyll a-binding protein 1, chloroplastic
Similarity search - Component
Biological speciesAmphidinium carterae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å
AuthorsHofmann, E. / Welte, W. / Diederichs, K.
Citation
Journal: Science / Year: 1996
Title: Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae.
Authors: Hofmann, E. / Wrench, P.M. / Sharples, F.P. / Hiller, R.G. / Welte, W. / Diederichs, K.
#1: Journal: FEBS Lett. / Year: 1990
Title: Crystallization and Preliminary X-Ray Analysis of a Peridinin-Chlorophyll a Protein from Amphidinium Carterae
Authors: Steck, K. / Wacker, T. / Welte, W. / Sharples, F.P. / Hiller, R.G.
History
DepositionMar 6, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 17, 2011Group: Other
Revision 2.0Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / pdbx_validate_chiral / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: PERIDININ-CHLOROPHYLL PROTEIN
N: PERIDININ-CHLOROPHYLL PROTEIN
O: PERIDININ-CHLOROPHYLL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,80139
Polymers97,6053
Non-polymers26,19636
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.426, 116.296, 67.025
Angle α, β, γ (deg.)90.00, 94.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.49854, -0.86687, 0.00145), (0.86687, -0.49853, 0.00261), (-0.00155, 0.00256, 1)153.34306, 46.75932, -0.2864
2given(-0.50059, 0.86564, 0.00864), (-0.86533, -0.50064, 0.02349), (0.02466, 0.00428, 0.99969)36.13253, 155.98816, -1.8953

-
Components

#1: Protein PERIDININ-CHLOROPHYLL PROTEIN / PCP


Mass: 32535.066 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote) / Strain: CS-21 / References: UniProt: P80484
#2: Chemical
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#3: Chemical...
ChemComp-PID / PERIDININ / Peridinin


Mass: 630.810 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C39H50O7
#4: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C51H96O15
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 56 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
24-6 %PEG80001drop
3100 mM1dropMgCl2
450 mM1dropKCl
524 mMtriethylammoniumphosphate1drop
650 mMTris-HCl1drop
78-12 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.865
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 16, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.865 Å / Relative weight: 1
ReflectionResolution: 2→33.8 Å / Num. obs: 96045 / % possible obs: 92.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.19 / % possible all: 92.6
Reflection shell
*PLUS
% possible obs: 82.4 % / Rmerge(I) obs: 0.265

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SIR / Resolution: 2→40 Å / Cross valid method: R-FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2325 2.45 %SHELLS
Rwork0.179 ---
obs0.179 94989 92.5 %-
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 1890 416 9152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight Biso Weight position
11RESTRAINTS, APPLIED TO M, N, OX-RAY DIFFRACTION3400
22X-RAY DIFFRACTION3200
33X-RAY DIFFRACTION2100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2EPAR.CHROMOETOP.CHROMO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 93720
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.68

+
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