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- PDB-2rcr: STRUCTURE OF THE MEMBRANE-BOUND PROTEIN PHOTOSYNTHETIC REACTION C... -

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Basic information

Entry
Database: PDB / ID: 2rcr
TitleSTRUCTURE OF THE MEMBRANE-BOUND PROTEIN PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES
Components(PHOTOSYNTHETIC REACTION CENTER ...Photosynthetic reaction centre) 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 / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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 centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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.

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Components

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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

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Non-polymers , 4 types, 9 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


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


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 / Iron


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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