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- PDB-5lri: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH ... -

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Basic information

Entry
Database: PDB / ID: 5lri
TitlePHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH TRP (CHAIN L, EL212W)
Components(Reaction center protein ...) x 3
KeywordsELECTRON TRANSPORT / TRANSMEMBRANE / PHOTOSYNTHESIS
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 / nonane / : / SPEROIDENONE / 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: 2.4 Å
AuthorsFyfe, P.K. / Jones, M.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I022570/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilB13439 United Kingdom
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: On the mechanism of ubiquinone mediated photocurrent generation by a reaction center based photocathode.
Authors: Friebe, V.M. / Swainsbury, D.J. / Fyfe, P.K. / van der Heijden, W. / Jones, M.R. / Frese, R.N.
History
DepositionAug 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)104,66622
Polymers93,8683
Non-polymers10,79819
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38030 Å2
ΔGint-236 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.820, 139.820, 185.252
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: 31403.486 Da / Num. of mol.: 1 / Mutation: E212W
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION EL212W
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: pufL, RHOS4_18610, RSP_0257 / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): EL212W / References: UniProt: Q3J1A5
#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 genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: pufM, RHOS4_18600, RSP_0256 / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): EL212W / References: UniProt: Q3J1A6
#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 genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: puhA, RHOS4_18960, RSP_0291 / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): EL212W / References: UniProt: Q3J170

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Non-polymers , 9 types, 311 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-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H20
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#10: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 5.2 Å3/Da / Density % sol: 74.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Well containing 9 mg mL-1 RC, 0.09 % v/v LDAO, 3.5 % w/v 1,2,3-heptanetriol, and 0.75 M potassium phosphate (pH 7.5) equilibrated against 1.5 M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→18 Å / Num. obs: 77800 / % possible obs: 95 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.63 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild Type RHODOBACTER SPHAEROIDESCOORDINATES (UNPUBLISHED DATA)

Resolution: 2.4→17.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.229 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21749 3863 5 %RANDOM
Rwork0.18899 ---
obs0.19044 73853 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å20 Å2
2--0.45 Å20 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.4→17.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6455 0 716 292 7463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027467
X-RAY DIFFRACTIONr_bond_other_d0.0020.027143
X-RAY DIFFRACTIONr_angle_refined_deg1.7632.04210205
X-RAY DIFFRACTIONr_angle_other_deg1.061316370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77822.58283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44915973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5021532
X-RAY DIFFRACTIONr_chiral_restr0.1930.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218092
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021753
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7993.9053287
X-RAY DIFFRACTIONr_mcbond_other1.7983.9033286
X-RAY DIFFRACTIONr_mcangle_it2.7895.8484107
X-RAY DIFFRACTIONr_mcangle_other2.7895.854108
X-RAY DIFFRACTIONr_scbond_it2.1244.414180
X-RAY DIFFRACTIONr_scbond_other2.1244.4114181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3666.4616098
X-RAY DIFFRACTIONr_long_range_B_refined5.47434.2838966
X-RAY DIFFRACTIONr_long_range_B_other5.47434.2888967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 302 -
Rwork0.262 5251 -
obs--94.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40280.4375-0.41130.6847-0.43150.464-0.14220.0578-0.1639-0.1284-0.0006-0.14520.1244-0.10270.14280.05930.02470.06950.22570.00940.0842-3.7601-66.760161.8504
20.41440.1546-0.3130.0679-0.08030.6210.08050.09640.11780.03820.06990.0542-0.0729-0.0462-0.15040.02910.05720.05120.21820.04930.1335-12.8726-47.053459.4098
30.48270.2227-0.3140.23460.04450.57310.04960.01330.01060.0849-0.01450.01190.0267-0.1432-0.03510.04260.03760.00890.22430.01540.0388-27.8644-70.662277.8385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 704
2X-RAY DIFFRACTION2M3 - 302
3X-RAY DIFFRACTION3H11 - 249

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