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- PDB-1pst: CRYSTALLOGRAPHIC ANALYSES OF SITE-DIRECTED MUTANTS OF THE PHOTOSY... -

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Basic information

Entry
Database: PDB / ID: 1pst
TitleCRYSTALLOGRAPHIC ANALYSES OF SITE-DIRECTED MUTANTS OF THE PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES
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 / 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 / SPIRILLOXANTHIN / : / 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: 3 Å
AuthorsChirino, A.J. / Feher, G. / Rees, D.C.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic analyses of site-directed mutants of the photosynthetic reaction center from Rhodobacter sphaeroides.
Authors: Chirino, A.J. / Lous, E.J. / Huber, M. / Allen, J.P. / Schenck, C.C. / Paddock, M.L. / Feher, G. / Rees, D.C.
#1: 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.
#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: Nature / Year: 1989
Title: Structure and Function of Bacterial Photosynthetic Reaction Centers
Authors: Feher, G. / Allen, J.P. / Okamura, M.Y. / Rees, D.C.
#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: Membrane-Protein Interactions
Authors: Yeates, T.O. / Komiya, H. / Rees, D.C. / Allen, J.P. / Feher, G.
#7: 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.
#8: 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.
#9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Structure Homology of the Reaction Center from Rhodopseudomonas Sphaeroides and Rhodopseudomonas Viridis as Determined by X-Ray Diffraction
Authors: Allen, J.P. / Feher, G. / Yeates, T.O. / Rees, D.C. / Desenhofer, J. / Michel, H. / Huber, R.
History
DepositionDec 13, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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_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.pdbx_dist_value / _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_ref_seq_dif.details / _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
M: PHOTOSYNTHETIC REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,45313
Polymers88,6713
Non-polymers7,78210
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30450 Å2
ΔGint-233 kcal/mol
Surface area30150 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: LEU L 269 - PRO L 270 OMEGA = 92.80 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO M 49
3: ASN M 81 - PRO M 82 OMEGA =146.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: PRO M 96 - PRO M 97 OMEGA =146.22 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO M 99
6: TYR H 40 - PRO H 41 OMEGA =307.71 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: PHE H 56 - PRO H 57 OMEGA =303.58 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: LEU H 58 - PRO H 59 OMEGA =217.93 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: CIS PROLINE - PRO H 76
10: ARG H 83 - PRO H 84 OMEGA =245.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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

#1: Protein PHOTOSYNTHETIC REACTION CENTER / Photosynthetic reaction centre


Mass: 29795.633 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 / Photosynthetic reaction centre


Mass: 33184.258 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 / Photosynthetic reaction centre


Mass: 25691.557 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 , 5 types, 10 molecules

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


Mass: 911.504 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#5: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6
#6: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


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
#8: Chemical ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H60O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 22184 / % possible obs: 71.1 % / Num. measured all: 67299 / Rmerge(I) obs: 0.103

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.218 / Rfactor obs: 0.218 / Highest resolution: 3 Å
Details: THE STRUCTURE OF THE H-CHAIN IS BASED MAINLY ON MOLECULAR REPLACEMENT FROM THE RPS. VIRIDIS REACTION CENTER STRUCTURE AND IS LESS RELIABLE THAN REST OF THE STRUCTURE. IN GENERAL THE ...Details: THE STRUCTURE OF THE H-CHAIN IS BASED MAINLY ON MOLECULAR REPLACEMENT FROM THE RPS. VIRIDIS REACTION CENTER STRUCTURE AND IS LESS RELIABLE THAN REST OF THE STRUCTURE. IN GENERAL THE TRANSMEMBRANE REGION OF THE STRUCTURE IS MORE RELIABLE THAN THE HYDROPHILIC REGIONS OF THE MOLECULE.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 498 0 6786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Num. reflection obs: 17962 / σ(F): 2 / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.35

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