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- PDB-4rcr: STRUCTURE OF THE REACTION CENTER FROM RHODOBACTER SPHAEROIDES R-2... -

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Entry
Database: PDB / ID: 4rcr
TitleSTRUCTURE OF THE REACTION CENTER FROM RHODOBACTER SPHAEROIDES R-26 AND 2.4.1: PROTEIN-COFACTOR (BACTERIOCHLOROPHYLL, BACTERIOPHEOPHYTIN, AND CAROTENOID) INTERACTIONS
Components(PHOTOSYNTHETIC REACTION ...) 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 / : / UBIQUINONE-10 / 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: 2.8 Å
AuthorsKomiya, H. / Yeates, T.O. / Chirino, A.J. / Rees, D.C. / Allen, J.P. / Feher, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions.
Authors: Yeates, T.O. / Komiya, H. / Chirino, A. / Rees, D.C. / Allen, J.P. / Feher, G.
#1: Journal: Nature / Year: 1989
Title: Structure and Function of Bacterial Photosynthetic Reaction Centres
Authors: Feher, G. / Allen, J.P. / Okamura, M.Y. / Rees, D.C.
#2: Journal: Annu.Rev.Biochem. / Year: 1989
Title: The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins
Authors: Rees, D.C. / Komiya, H. / Yeates, T.O. / Allen, J.P. / Feher, G.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of the Reaction Center from Rhodobacter Sphaeroides R-26 and 2.4.1: Symmetry Relations and Sequence Comparisons between Different Species
Authors: Komiya, H. / Yeates, T.O. / Rees, D.C. / Allen, J.P. / Feher, G.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Protein-Cofactor (Quinones and Fe2+) Interactions
Authors: Allen, J.P. / Feher, G. / Yeates, T.O. / Komiya, H. / Rees, D.C.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Protein Subunits
Authors: Allen, J.P. / Feher, G. / Yeates, T.O. / Komiya, H. / Rees, D.C.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Cofactors
Authors: Allen, J.P. / Feher, G. / Yeates, T.O. / Komiya, H. / Rees, D.C.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Membrane-Protein Interactions
Authors: Yeates, T.O. / Komiya, H. / Rees, D.C. / Allen, J.P. / Feher, G.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Structural Homology of Reaction Centers from Rhodopseudomonas Sphaeroides and Rhodopseudomonas Viridis as Determined by X-Ray Diffraction
Authors: Allen, J.P. / Feher, G. / Yeates, T.O. / Rees, D.C. / Deisenhofer, J. / Michel, H. / Huber, R.
#9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Crystallization of Reaction Center from Rhodopseudomonas Sphaeroides: Preliminary Characterization
Authors: Allen, J.P. / Feher, G.
History
DepositionSep 9, 1991Processing site: BNL
Revision 1.0Oct 31, 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 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PHOTOSYNTHETIC REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,31113
Polymers93,8113
Non-polymers7,49910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28980 Å2
ΔGint-220 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.000, 77.500, 141.800
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 49 AND PRO M 99 ARE CIS PROLINES.

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Components

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

#1: Protein PHOTOSYNTHETIC REACTION CENTER


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


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


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

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Sugars , 1 types, 1 molecules

#7: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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-U10 / UBIQUINONE-10 / Coenzyme Q10


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


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

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Details: taken from Allen, J.P. et al (1986). Proc. Natl. Acad. Sci., 83, 8589-8593.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.36 M1dropNaCl
33.9 %(w/v)heptane triol1drop
412 %(w/v)PEG40001drop
50.06 %lauryldmethylamine oxide1drop
615 mMTris chloride1drop
71 mMEDTA1drop
80.1 %1dropNaN3
90.6 M1reservoirNaCl
1022 %PEG40001reservoir
1115 mMTris chloride1reservoir
121 mMEDTA1reservoir
130.1 %1reservoirNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Num. obs: 23025 / % possible obs: 74 % / Num. measured all: 73313 / Rmerge(I) obs: 0.14

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→8 Å
Details: THE STRUCTURE OF H-CHAIN IS BASED MAINLY ON MOLECULAR REPLACEMENT FROM THE (RHODOPSEUDOMONAS) VIRIDIS REACTION CENTER AND IS LESS RELIABLE THAN THE REST OF THE STRUCTURE. IN GENERAL, THE ...Details: THE STRUCTURE OF H-CHAIN IS BASED MAINLY ON MOLECULAR REPLACEMENT FROM THE (RHODOPSEUDOMONAS) VIRIDIS REACTION CENTER AND IS LESS RELIABLE THAN THE REST OF THE STRUCTURE. IN GENERAL, THE TRANSMEMBRANE REGION OF THE STRUCTURE IS MORE RELIABLE THAN THE HYDROPHILIC REGIONS OF THE MOLECULE.
RfactorNum. reflection
Rwork0.227 -
obs-21992
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 477 0 6764
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Num. reflection obs: 21992 / Rfactor obs: 0.263 / Rfactor Rwork: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.026
X-RAY DIFFRACTIONo_angle_deg5.5

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