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- PDB-2hg9: Reaction centre from Rhodobacter sphaeroides strain R-26.1 comple... -

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Basic information

Entry
Database: PDB / ID: 2hg9
TitleReaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with tetrabrominated phosphatidylcholine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS/MEMBRANE PROTEIN / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / LIPID BINDING SITES / BROMINATED LIPIDS / MEMBRANE PROTEIN / PHOTOSYNTHESIS-MEMBRANE PROTEIN COMPLEX
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 / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / 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; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / 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 / CARDIOLIPIN / : / : / Chem-PC7 / Chem-PCK / PHOSPHATE ION / UBIQUINONE-10 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / : / Chem-PC7 / Chem-PCK / PHOSPHATE ION / UBIQUINONE-10 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRoszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J.
CitationJournal: Biochemistry / Year: 2007
Title: Brominated Lipids Identify Lipid Binding Sites on the Surface of the Reaction Center from Rhodobacter sphaeroides.
Authors: Roszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)107,00035
Polymers93,8113
Non-polymers13,18932
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40890 Å2
ΔGint-271 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.554, 139.554, 184.609
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 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.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y8
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34398.543 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.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y9
#3: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28066.322 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.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y7

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Non-polymers , 13 types, 473 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#8: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#9: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#11: Chemical ChemComp-PCK / (7R,18S,19R)-18,19-DIBROMO-7-{[(9S,10S)-9,10-DIBROMOOCTADECANOYL]OXY}-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-P HOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE / TETRABROMINATED PHOSPHATIDYLCHOLINE / 1,2-DISTEAROYL(9,10-DIBROMO)-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 1106.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85Br4NO8P
#12: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#13: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#14: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#15: Chemical ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC


Mass: 763.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 5.52 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Potassium phosphate, LDAO, 1,2,3-heptanetriol, dioxane, 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: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2004 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.45→39.37 Å / Num. obs: 76588 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.8 / Num. unique all: 11112 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished structure of reaction centre at 1.95A resolution

Resolution: 2.45→39.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.135 / SU ML: 0.115 / 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: 0.198 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; the above average isotropic B value is an average residual B after TLS refinement while the final average atomic B is 55.5
RfactorNum. reflection% reflectionSelection details
Rfree0.20914 3709 4.9 %RANDOM
Rwork0.1788 ---
all0.18035 75227 --
obs0.18035 71518 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 853 441 7769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227653
X-RAY DIFFRACTIONr_bond_other_d0.0010.025263
X-RAY DIFFRACTIONr_angle_refined_deg1.7382.05510424
X-RAY DIFFRACTIONr_angle_other_deg1.2443.00312601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20822.664289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.632151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0811533
X-RAY DIFFRACTIONr_chiral_restr0.1050.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021563
X-RAY DIFFRACTIONr_nbd_refined0.2210.21686
X-RAY DIFFRACTIONr_nbd_other0.2010.25321
X-RAY DIFFRACTIONr_nbtor_refined0.1960.23618
X-RAY DIFFRACTIONr_nbtor_other0.0920.23448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.216
X-RAY DIFFRACTIONr_mcbond_it0.7511.54085
X-RAY DIFFRACTIONr_mcbond_other0.1951.51689
X-RAY DIFFRACTIONr_mcangle_it1.35326542
X-RAY DIFFRACTIONr_scbond_it2.3333623
X-RAY DIFFRACTIONr_scangle_it3.3074.53877
X-RAY DIFFRACTIONCruickshank estimated coordinate error0.198
X-RAY DIFFRACTIONMaximum Likelihood estimated coordinate error0.115
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 271 -
Rwork0.224 5233 -
obs-5233 98.15 %
Refinement TLS params.Method: refined / Origin x: 56.0554 Å / Origin y: 60.6887 Å / Origin z: 65.0923 Å
111213212223313233
T-0.2879 Å20.0768 Å20.0402 Å2--0.0106 Å20.0144 Å2---0.1762 Å2
L1.4063 °20.5871 °2-0.5787 °2-1.2054 °2-0.4162 °2--1.0894 °2
S-0.0257 Å °0.0716 Å °0.0363 Å °-0.0842 Å °0.0688 Å °-0.0411 Å °-0.0683 Å °-0.0911 Å °-0.0431 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 281
2X-RAY DIFFRACTION1M1 - 301
3X-RAY DIFFRACTION1H11 - 251
4X-RAY DIFFRACTION1M311 - 313
5X-RAY DIFFRACTION1L312 - 314
6X-RAY DIFFRACTION1M401
7X-RAY DIFFRACTION1L402
8X-RAY DIFFRACTION1M500
9X-RAY DIFFRACTION1M501
10X-RAY DIFFRACTION1L502
11X-RAY DIFFRACTION1H700 - 709
12X-RAY DIFFRACTION1M701 - 711
13X-RAY DIFFRACTION1L703 - 712
14X-RAY DIFFRACTION1H801
15X-RAY DIFFRACTION1M800 - 802
16X-RAY DIFFRACTION1H901 - 908
17X-RAY DIFFRACTION1M902 - 920
18X-RAY DIFFRACTION1H1001 - 1441
19X-RAY DIFFRACTION1M1004 - 1440
20X-RAY DIFFRACTION1L1002 - 1428

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