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

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Basic information

Entry
Database: PDB / ID: 1aig
TitlePHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE D+QB-CHARGE SEPARATED STATE
Components(PHOTOSYNTHETIC REACTION CENTER ...) x 3
KeywordsPHOTOSYNTHETIC REACTION CENTER / INTEGRAL MEMBRANE PROTEIN / CHARGE SEPARATED
Function / homology
Function and homology information


: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / 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 REPLACEMENT / Resolution: 2.6 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: 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.
#2: 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.
#3: 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.
#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 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.
#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 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: The Protein Subunits
Authors: Allen, J.P. / Feher, G. / Yeates, T.O. / Komiya, H. / Rees, D.C.
#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 17, 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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 (L SUBUNIT)
M: PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
H: PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)
N: PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)
O: PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
P: PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,17924
Polymers187,7656
Non-polymers14,41418
Water1,54986
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)101,08912
Polymers93,8823
Non-polymers7,2079
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31180 Å2
ΔGint-225 kcal/mol
Surface area30220 Å2
MethodPISA
2
N: PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)
O: PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
P: 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 area31090 Å2
ΔGint-230 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.100, 140.100, 271.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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

#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 , 5 types, 104 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


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


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsELECTRON DENSITY FOR THE UBIQUINONE-10 MOLECULES IS WEAK BEYOND THE C16 CARBON OF QB IN MOLECULE 1 ...ELECTRON DENSITY FOR THE UBIQUINONE-10 MOLECULES IS WEAK BEYOND THE C16 CARBON OF QB IN MOLECULE 1 AND THE C36 CARBON OF QA IN MOLECULE 1.

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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: 3.64 Å3/Da / Density % sol: 66 %
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: 2.6→30 Å / Num. obs: 74104 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.085 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.72 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.16 / % possible all: 86
Reflection
*PLUS
Num. measured all: 203621 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
Rmerge(I) obs: 0.16

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Processing

Software
NameVersionClassification
MERLOTphasing
X-PLOR3.89refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3658 5 %RANDOM
Rwork0.215 ---
obs0.215 71316 88 %-
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13010 0 1042 86 14138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
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: 2.6→2.72 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.343 431 4.2 %
Rwork0.334 8181 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARM_RC2.PROTOPH_RC2.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.89 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.07

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