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- PDB-1aij: PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN TH... -

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Basic information

Entry
Database: PDB / ID: 1aij
TitlePHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE
Components(PHOTOSYNTHETIC REACTION CENTER ...Photosynthetic reaction centre) x 3
KeywordsPHOTOSYNTHETIC REACTION CENTER / INTEGRAL MEMBRANE PROTEIN / CHARGE NEUTRAL
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 / : / 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 / SYNCHROTRON / MOLECULAR / Resolution: 2.2 Å
AuthorsStowell, M.H.B. / Mcphillips, T.M. / Soltis, S.M. / Rees, D.C. / Abresch, E. / Feher, G.
Citation
Journal: Science / Year: 1997
Title: Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer.
Authors: Stowell, M.H. / McPhillips, T.M. / Rees, D.C. / Soltis, S.M. / Abresch, E. / 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: Protein-Cofactor (Bacteriochlorophyll, Bacteriopheophytin, and Carotenoid) Interactions
Authors: Yeates, T.O. / Komiya, H. / Chirino, A. / 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 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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.
#9: 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.
#10: 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
DepositionApr 18, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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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)
R: PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)
S: PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
T: PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,09628
Polymers187,7656
Non-polymers15,33222
Water8,431468
1
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)102,00716
Polymers93,8823
Non-polymers8,12513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32850 Å2
ΔGint-213 kcal/mol
Surface area29830 Å2
MethodPISA
2
R: PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)
S: PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
T: PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,08912
Polymers93,8823
Non-polymers7,2079
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29370 Å2
ΔGint-219 kcal/mol
Surface area30190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.080, 140.080, 271.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.00114, 0.00196), (-0.00226, -0.5211, 0.85349), (5.0E-5, -0.8535, -0.5211)
Vector: -39.69329, 61.21699, 141.10367)

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Components

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PHOTOSYNTHETIC REACTION CENTER ... , 3 types, 6 molecules LRMSHT

#1: Protein PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)


Mass: 31346.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)


Mass: 34398.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)


Mass: 28137.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

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Non-polymers , 6 types, 490 molecules

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


Mass: 911.504 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#5: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#6: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Details: Allen, J.P., (1994) Proteins. Struct. Funct. Genet., 20, 283.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-Cl1drop
30.85 %beta-octylglucoside1drop
46.0 %PEG40001drop
50.4 %amphiphiles benzamidine hydrochloride1drop
62.5 %heptane triol1drop
732 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: BENT
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 114087 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.056
Reflection
*PLUS
Num. measured all: 335463 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Rmerge(I) obs: 0.146

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Processing

Software
NameVersionClassification
MERLOTphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5884 5 %RANDOM
Rwork0.216 ---
obs0.216 112334 --
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12996 0 929 468 14393
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
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
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.342 373 5 %
Rwork0.323 7026 -
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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