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- PDB-5lse: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH Glu L212 replaced with... -

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Basic information

Entry
Database: PDB / ID: 5lse
TitlePHOTOSYNTHETIC REACTION CENTER MUTANT WITH Glu L212 replaced with Ala (CHAIN L, EL212W), Asp L213 replaced with ALA (Chain L, DL213A) AND LEU M215 REPLACED WITH ALA (CHAIN M, LM215A)
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, H subunit, N-terminal / PRC-barrel domain ...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, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / 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 / DODECANE / : / PHOSPHATE ION / 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: 2.5 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 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1May 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)104,56823
Polymers93,6673
Non-polymers10,90120
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38830 Å2
ΔGint-195 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.993, 138.993, 184.711
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: 31244.346 Da / Num. of mol.: 1 / Mutation: EL212A, DL213A
Source method: isolated from a genetically manipulated source
Details: Glu L212 to Ala engineered mutation Asp L213 to Ala engineered mutation
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides (bacteria) / Variant (production host): EL212A/DL213A/LM215A / References: UniProt: P0C0Y8
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34356.461 Da / Num. of mol.: 1 / Mutation: LM215A
Source method: isolated from a genetically manipulated source
Details: Leu M215 ALA engineered mutation / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: pRKEH10D / Production host: Rhodobacter sphaeroides (bacteria) / 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 genetically manipulated source
Details: Missing N and C-terminal residues unobserved in electron density
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides (bacteria) / Variant (production host): EL212A/DL213A/LM215A / References: UniProt: P0C0Y7

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Non-polymers , 10 types, 290 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-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26
#8: Chemical ChemComp-FE / FE (III) ION


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


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#10: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#11: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.5→23.9 Å / Num. obs: 70501 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE RHODOBACTER SPHAEROIDES COORDINATES (Unpublished data)

Resolution: 2.5→23.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.34 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20118 3515 5 %RANDOM
Rwork0.16769 ---
obs0.16934 67435 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.5→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6447 0 710 270 7427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027430
X-RAY DIFFRACTIONr_bond_other_d0.0020.027107
X-RAY DIFFRACTIONr_angle_refined_deg1.8362.04110150
X-RAY DIFFRACTIONr_angle_other_deg1.088316283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18922.545279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55315966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.511532
X-RAY DIFFRACTIONr_chiral_restr0.2030.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218064
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021745
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_it1.8563.733286
X-RAY DIFFRACTIONr_mcbond_other1.8523.7283285
X-RAY DIFFRACTIONr_mcangle_it2.9795.5854104
X-RAY DIFFRACTIONr_mcangle_other2.9795.5884105
X-RAY DIFFRACTIONr_scbond_it2.5474.2534143
X-RAY DIFFRACTIONr_scbond_other2.5394.2534143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0226.2166046
X-RAY DIFFRACTIONr_long_range_B_refined5.82132.4988864
X-RAY DIFFRACTIONr_long_range_B_other5.82632.5038865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 253 -
Rwork0.256 4903 -
obs--98.42 %
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)
10.9395-0.0876-0.2310.37290.11060.4331-0.0040.0878-0.2145-0.014-0.01820.068-0.0418-0.01410.02220.09920.02440.03260.0158-0.01490.069210.139290.2467-154.2491
20.9262-0.1759-0.23210.63050.0650.56860.03930.02510.1115-0.02950.03-0.1308-0.10860.0923-0.06930.121-0.00850.05060.0224-0.00690.048422.9797108.0407-156.1966
30.93010.09260.05670.54180.00140.49860.0049-0.09880.03050.08130.03650.1246-0.1002-0.0186-0.04140.15920.03950.05570.02210.01510.0388-5.0976109.2067-137.9903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 281
2X-RAY DIFFRACTION2M3 - 302
3X-RAY DIFFRACTION3H11 - 250

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