[English] 日本語
Yorodumi
- PDB-1pyh: Crystal structure of RC-LH1 core complex from Rhodopseudomonas pa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pyh
TitleCrystal structure of RC-LH1 core complex from Rhodopseudomonas palustris
Components
  • (Light-harvesting protein B-800/850, ...) x 2
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
KeywordsPHOTOSYNTHESIS / bacterial photosynthetic core complex / integral membrane proteins / light harvesting complex / reaction centre
Function / homologyBACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / :
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.8 Å
AuthorsRoszak, A.W. / Howard, T.D. / Southall, J. / Gardiner, A.T. / Law, C.J. / Isaacs, N.W. / Cogdell, R.J.
CitationJournal: Science / Year: 2003
Title: Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris.
Authors: Roszak, A.W. / Howard, T.D. / Southall, J. / Gardiner, A.T. / Law, C.J. / Isaacs, N.W. / Cogdell, R.J.
History
DepositionJul 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600heterogen A 19 carbon tail is missing from all the BCL ligands numbered 1-32
Remark 999sequence No suitable sequence database reference was available at the time of processing this structure.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reaction center protein L chain
B: Reaction center protein M chain
C: Reaction center protein H chain
D: Light-harvesting protein B-800/850, alpha chain
E: Light-harvesting protein B-800/850, beta chain
F: Light-harvesting protein B-800/850, alpha chain
G: Light-harvesting protein B-800/850, beta chain
H: Light-harvesting protein B-800/850, alpha chain
I: Light-harvesting protein B-800/850, beta chain
J: Light-harvesting protein B-800/850, alpha chain
K: Light-harvesting protein B-800/850, beta chain
L: Light-harvesting protein B-800/850, alpha chain
M: Light-harvesting protein B-800/850, beta chain
N: Light-harvesting protein B-800/850, alpha chain
O: Light-harvesting protein B-800/850, beta chain
P: Light-harvesting protein B-800/850, alpha chain
Q: Light-harvesting protein B-800/850, beta chain
R: Light-harvesting protein B-800/850, alpha chain
S: Light-harvesting protein B-800/850, beta chain
T: Light-harvesting protein B-800/850, alpha chain
U: Light-harvesting protein B-800/850, beta chain
V: Light-harvesting protein B-800/850, alpha chain
W: Light-harvesting protein B-800/850, beta chain
X: Light-harvesting protein B-800/850, alpha chain
Y: Light-harvesting protein B-800/850, beta chain
Z: Light-harvesting protein B-800/850, alpha chain
1: Light-harvesting protein B-800/850, alpha chain
2: Light-harvesting protein B-800/850, beta chain
3: Light-harvesting protein B-800/850, alpha chain
4: Light-harvesting protein B-800/850, beta chain
5: Light-harvesting protein B-800/850, alpha chain
6: Light-harvesting protein B-800/850, beta chain
7: Light-harvesting protein B-800/850, alpha chain
8: Light-harvesting protein B-800/850, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,26571
Polymers144,43934
Non-polymers32,82537
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.037, 119.024, 130.432
Angle α, β, γ (deg.)69.32, 72.69, 66.52
Int Tables number1
Space group name H-MP1

-
Components

-
Reaction center protein ... , 3 types, 3 molecules ABC

#1: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 23932.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: strain 2.1.6
#2: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 25719.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: strain 2.1.6
#3: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 20528.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: strain 2.1.6

-
Light-harvesting protein B-800/850, ... , 2 types, 31 molecules DFHJLNPRTVXZ1357EGIKMOQSUWY2468

#4: Protein/peptide
Light-harvesting protein B-800/850, alpha chain / Antenna pigment protein / alpha chain


Mass: 2230.741 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: strain 2.1.6
#5: Protein/peptide
Light-harvesting protein B-800/850, beta chain / Antenna pigment protein / beta chain


Mass: 2571.161 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: strain 2.1.6

-
Non-polymers , 3 types, 37 molecules

#6: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#7: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#8: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 283 K / pH: 8.5
Details: MMe PEG 2000, sucrose monocholate, magnesium chloride, spermidine, TRIS HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283-289K, pH 8.50
Crystal grow
*PLUS
Temperature: 10-16 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5 %(w/v)sucrose monocholate1drop
21 %(w/v)spermidine1drop
310 mM1dropMgCl2
4100 mMTris-HCl1droppH8.5
58 %(w/v)PEG2000 MME1drop
616-25 %(w/v)PEG2000 MME1reservoir
720 mM1reservoirMgCl2
8100 mMTris-HCl1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 4.8→60 Å / Num. obs: 18334 / % possible obs: 97.3 % / Observed criterion σ(I): 1.1 / Redundancy: 2 % / Biso Wilson estimate: 228 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.3
Reflection shellResolution: 4.8→4.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.1 / % possible all: 83.4
Reflection
*PLUS
Highest resolution: 4.8 Å / Lowest resolution: 60 Å / Num. obs: 18335 / Num. measured all: 37214
Reflection shell
*PLUS
Highest resolution: 4.8 Å / % possible obs: 83.4 % / Mean I/σ(I) obs: 1.1

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REACTION CENTRE

Resolution: 4.8→60 Å / Cor.coef. Fo:Fc: 0.771 / Cor.coef. Fo:Fc free: 0.718 / SU B: 242.322 / SU ML: 3.026 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R: 1.756 / ESU R Free: 1.846 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.49131 944 5.1 %RANDOM
Rwork0.46745 ---
obs0.4687 17390 97.28 %-
all-17391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 198.26 Å2
Baniso -1Baniso -2Baniso -3
1--16.96 Å20.98 Å2-0.35 Å2
2--23.77 Å2-5.53 Å2
3----3.47 Å2
Refinement stepCycle: LAST / Resolution: 4.8→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8295 0 1805 0 10100
LS refinement shellResolution: 4.8→5.058 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.576 139
Rwork0.554 2279
Software
*PLUS
Version: 5.2.0000 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5.15 % / Rfactor Rfree: 0.484 / Rfactor Rwork: 0.463
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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