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- PDB-1rgn: Structure of the reaction centre from Rhodobacter sphaeroides car... -

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Basic information

Entry
Database: PDB / ID: 1rgn
TitleStructure of the reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1 reconstituted with spheroidene
Components(Reaction center protein ...Photosynthetic reaction centre) x 3
KeywordsPHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / RECONSTITUTED CAROTENOID / CAROTENOID BINDING SITE / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / 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 / : / PHOSPHATE ION / SPHEROIDENE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PHOSPHATE ION / SPHEROIDENE / 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: 2.8 Å
AuthorsRoszak, A.W. / Frank, H.A. / McKendrick, K. / Mitchell, I.A. / Cogdell, R.J. / Isaacs, N.W.
CitationJournal: STRUCTURE / Year: 2004
Title: Protein Regulation of Carotenoid Binding: Gatekeeper and Locking Amino Acid Residues in Reaction Centers of Rhodobacter sphaeroides
Authors: Roszak, A.W. / McKendrick, K. / Gardiner, A.T. / Mitchell, I.A. / Isaacs, N.W. / Cogdell, R.J. / Hashimoto, H. / Frank, H.A.
History
DepositionNov 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.4Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 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_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_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

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Assembly

Deposited unit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,05920
Polymers93,8113
Non-polymers9,24717
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36700 Å2
ΔGint-232 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.817, 139.817, 184.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Reaction center protein ... , 3 types, 3 molecules LMH

#1: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid.IN THIS ENTRY R-26.1 HAS BEEN RECONSTITUTED WITH CAROTENOID SPHEROIDENE.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

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Non-polymers , 8 types, 190 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-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#7: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#8: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#10: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H60O
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 5.54 Å3/Da / Density % sol: 77.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Trisodium citrate, LDAO, 1,2,3-heptanetriol, ethylene glycol, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 1999 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→24 Å / Num. all: 46063 / Num. obs: 46063 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 79.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2377 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 19.4 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS thermal mode followed by the restrained refinement of atomic coordinates and isotropic B-factors; all details in the pdb-file.
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.403 / ESU R Free: 0.284
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron density quality some atoms at the end of the carbohydrate tails of ligands U10 were not modelled
RfactorNum. reflection% reflectionSelection details
Rfree0.23246 2277 5 %RANDOM
Rwork0.18859 ---
all0.1907 45563 --
obs0.19076 43286 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.611 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 0 634 173 7276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227379
X-RAY DIFFRACTIONr_bond_other_d0.0010.026899
X-RAY DIFFRACTIONr_angle_refined_deg1.9072.02110104
X-RAY DIFFRACTIONr_angle_other_deg1.169315874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42622.65283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94215975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.891532
X-RAY DIFFRACTIONr_chiral_restr0.1050.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021570
X-RAY DIFFRACTIONr_nbd_refined0.2170.21814
X-RAY DIFFRACTIONr_nbd_other0.1910.27485
X-RAY DIFFRACTIONr_nbtor_other0.0950.23940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.23
X-RAY DIFFRACTIONr_mcbond_it0.821.55155
X-RAY DIFFRACTIONr_mcbond_other0.1311.51695
X-RAY DIFFRACTIONr_mcangle_it1.03926510
X-RAY DIFFRACTIONr_scbond_it1.53334180
X-RAY DIFFRACTIONr_scangle_it2.3534.53584
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.328 172
Rwork0.254 3295
obs-3295
Refinement TLS params.Method: refined / Origin x: 10.973 Å / Origin y: 102.5517 Å / Origin z: 33.5605 Å
111213212223313233
T0.0321 Å20.1712 Å20.0257 Å2--0.3689 Å2-0.0308 Å2---0.2323 Å2
L2.1604 °2-0.3699 °2-0.6867 °2-0.8816 °20.1951 °2--1.4827 °2
S0.0735 Å °0.18 Å °-0.0198 Å °-0.0095 Å °-0.0202 Å °-0.0672 Å °-0.1285 Å °0.012 Å °-0.0532 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 281
2X-RAY DIFFRACTION1M1 - 302
3X-RAY DIFFRACTION1H11 - 250
4X-RAY DIFFRACTION1M401
5X-RAY DIFFRACTION1L402
6X-RAY DIFFRACTION1M500
7X-RAY DIFFRACTION1M501
8X-RAY DIFFRACTION1L502
9X-RAY DIFFRACTION1M600

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