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

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Entry
Database: PDB / ID: 2hit
TitleReaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylethanolamine
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-PEV / Chem-PEW / PHOSPHATE ION / UBIQUINONE-10 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / : / Chem-PEV / Chem-PEW / 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: 2.75 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 29, 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 / 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_conn.ptnr2_label_seq_id / _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)106,07130
Polymers93,8113
Non-polymers12,26027
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39310 Å2
ΔGint-279 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.289, 139.289, 183.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11H-1293-

HOH

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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, 421 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


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


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-FE / FE (III) ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#11: 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
#12: Chemical ChemComp-PEW / (1R)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (9S,10S)-9,10-DIBROMOOCTADECANOATE / DIBROMINATED PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-STEAROYL(9,10-DIBROMO)-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 877.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76Br2NO8P / Comment: phospholipid*YM
#13: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#14: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#15: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 5.48 Å3/Da / Density % sol: 77.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Potassium phosphate, LDAO, 1,2,3-heptanetriol, 1,2,3-hexanetriol, dioxane, NaCl, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91929 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2005 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91929 Å / Relative weight: 1
ReflectionResolution: 2.75→46.03 Å / Num. obs: 54102 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 74.5 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 23
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 4.3 / Num. unique all: 7805 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished structure of reaction centre at 1.95A resolution

Resolution: 2.75→46.01 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.317 / SU ML: 0.152 / 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: 0.319 / ESU R Free: 0.243 / 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 70.0
RfactorNum. reflection% reflectionSelection details
Rfree0.22193 2689 5 %RANDOM
Rwork0.1817 ---
all0.18369 54094 --
obs0.18369 51405 99.96 %-
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: 60.047 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 799 394 7687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227721
X-RAY DIFFRACTIONr_bond_other_d0.0020.025329
X-RAY DIFFRACTIONr_angle_refined_deg1.8782.05410526
X-RAY DIFFRACTIONr_angle_other_deg1.2743.00512646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4822.619294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.568151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.881534
X-RAY DIFFRACTIONr_chiral_restr0.1060.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021596
X-RAY DIFFRACTIONr_nbd_refined0.2320.21912
X-RAY DIFFRACTIONr_nbd_other0.2030.25594
X-RAY DIFFRACTIONr_nbtor_refined0.2030.23669
X-RAY DIFFRACTIONr_nbtor_other0.0930.23630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2461
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.213
X-RAY DIFFRACTIONr_mcbond_it0.6761.54126
X-RAY DIFFRACTIONr_mcbond_other0.1441.51706
X-RAY DIFFRACTIONr_mcangle_it1.2326625
X-RAY DIFFRACTIONr_scbond_it2.12733651
X-RAY DIFFRACTIONr_scangle_it3.1664.53897
X-RAY DIFFRACTIONCruickshank estimated coordinate error0.319
X-RAY DIFFRACTIONMaximum Likelihood estimated coordinate error0.152
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 164 -
Rwork0.188 3763 -
obs-3763 99.97 %
Refinement TLS params.Method: refined / Origin x: 10.999 Å / Origin y: 102.4614 Å / Origin z: 34.1604 Å
111213212223313233
T-0.0342 Å20.1181 Å20.0857 Å2--0.386 Å2-0.0331 Å2---0.3138 Å2
L3.0135 °2-0.5836 °2-0.8805 °2-1.3058 °20.1225 °2--1.3125 °2
S-0.0293 Å °0.178 Å °-0.2326 Å °0.0573 Å °0.0138 Å °0 Å °-0.1546 Å °-0.0108 Å °0.0155 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 281
2X-RAY DIFFRACTION1M1 - 302
3X-RAY DIFFRACTION1H9 - 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 - 708
12X-RAY DIFFRACTION1M701 - 706
13X-RAY DIFFRACTION1L707
14X-RAY DIFFRACTION1H801
15X-RAY DIFFRACTION1M800 - 802
16X-RAY DIFFRACTION1H901 - 904
17X-RAY DIFFRACTION1M902 - 920
18X-RAY DIFFRACTION1H1001 - 1391
19X-RAY DIFFRACTION1M1004 - 1392
20X-RAY DIFFRACTION1L1002 - 1394

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