[English] 日本語
Yorodumi
- PDB-2rcr: STRUCTURE OF THE MEMBRANE-BOUND PROTEIN PHOTOSYNTHETIC REACTION C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rcr
TitleSTRUCTURE OF THE MEMBRANE-BOUND PROTEIN PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES
Components(PHOTOSYNTHETIC REACTION CENTER ...) x 3
KeywordsPHOTOSYNTHETIC REACTION CENTER
Function / homology
Function and homology information


: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal ...Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Reaction center protein H chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsChang, C.-H. / Norris, J. / Schiffer, M.
Citation
Journal: Biochemistry / Year: 1991
Title: Structure of the membrane-bound protein photosynthetic reaction center from Rhodobacter sphaeroides.
Authors: Chang, C.H. / el-Kabbani, O. / Tiede, D. / Norris, J. / Schiffer, M.
#1: Journal: Biochemistry / Year: 1991
Title: Comparison of Reaction Centers from Rhodobacter Sphaeroides and Rhodobacter Viridis: Overall Architecture and Protein-Pigment Interactions
Authors: El-Kabbani, O. / Chang, C.-H. / Tiede, D. / Norris, J. / Schiffer, M.
History
DepositionFeb 4, 1991Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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
L: PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)
M: PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
H: PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,01812
Polymers93,8113
Non-polymers7,2079
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31740 Å2
ΔGint-230 kcal/mol
Surface area35450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.200, 139.600, 78.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO M 48 AND PRO H 41 ARE CIS PROLINES.

-
Components

-
PHOTOSYNTHETIC REACTION CENTER ... , 3 types, 3 molecules LMH

#1: Protein PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)


Mass: 31346.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)


Mass: 34398.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)


Mass: 28066.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

-
Non-polymers , 4 types, 9 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#5: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#6: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#7: Chemical ChemComp-FE / FE (III) ION


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.44 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(w/v)PEG40001drop
20.3 M1dropNaCl
310 mMTris-HCl1drop
40.8 %n-octyl-beta-D-glucopyranoside1drop
51 mMEDTA1drop
625 %(w/v)PEG40001reservoir
70.3 M1reservoirNaCl
810 mMPEG40001reservoir
91 mMEDTA1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 8 Å / Num. obs: 13493 / Observed criterion σ(F): 2.5 / Rmerge F obs: 0.09 / Num. measured all: 22866

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.22 / Highest resolution: 3.1 Å
Refinement stepCycle: LAST / Highest resolution: 3.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 491 0 7049
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0270.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.2630.3
X-RAY DIFFRACTIONp_multtor_nbd0.2960.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2450.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.53
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 8 Å / Num. reflection obs: 13493 / σ(F): 2.5 / Rfactor obs: 0.22
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