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- PDB-7mh4: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -

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Basic information

Entry
Database: PDB / ID: 7mh4
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-bromotyrosine
Components(Reaction center protein ...Photosynthetic reaction centre) x 3
KeywordsPHOTOSYNTHESIS / Photosynthetic / membrane protein / noncanonical amino acid / bromotyrosine
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 / metal ion binding
Similarity search - Function
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, 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.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / SPHEROIDENE / 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: 2.48 Å
AuthorsMathews, I. / Weaver, J. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Science Foundation (NSF, United States)1915727 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism.
Authors: Weaver, J.B. / Lin, C.Y. / Faries, K.M. / Mathews, I.I. / Russi, S. / Holten, D. / Kirmaier, C. / Boxer, S.G.
History
DepositionApr 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,51120
Polymers95,0883
Non-polymers10,42217
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Coordinate represent a complete multimer representing the biologically significant oligo merization state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35780 Å2
ΔGint-239 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.337, 141.337, 186.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11H-487-

HOH

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Components

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

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


Mass: 28923.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Plasmid: pIND4-RC-M210TAG-HaloY1 / Production host: Luteovulum sphaeroides (bacteria) / Strain (production host): RCx / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 31477.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Plasmid: pIND4-RC-M210TAG-HaloY1 / Production host: Luteovulum sphaeroides (bacteria) / Strain (production host): RCx / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 34687.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DBY - Tyr-210 modified to be 3,5-dibromotyrosine / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: pIND4-RC-M210TAG-HaloY1 / Production host: Luteovulum sphaeroides (bacteria) / Strain (production host): RCx / References: UniProt: P0C0Y9

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Non-polymers , 9 types, 261 molecules

#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe
#10: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C41H60O
#11: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C81H156O17P2 / Comment: phospholipid*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution; 1.4-1.5 M potassium phosphate reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 250 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2017 / Details: Rh coated collimating mirror, K-B focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.48→39 Å / Num. obs: 76551 / % possible obs: 99.6 % / Redundancy: 5.076 % / Biso Wilson estimate: 58.55 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.121 / Χ2: 1.039 / Net I/σ(I): 10.16 / Num. measured all: 388566 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.48-2.544.8551.0281.6927280563156190.5881.15499.8
2.54-2.615.3190.8592.1229182548854860.7050.954100
2.61-2.695.2980.6832.6328113531253060.7720.75999.9
2.69-2.775.2590.5833.0427368520952040.8240.64899.9
2.77-2.865.2480.4663.7326169499949860.8860.51999.7
2.86-2.965.2350.3724.6925514488948740.9120.41499.7
2.96-3.085.1630.2855.8424263471746990.9470.31799.6
3.08-3.24.8490.2276.9521596448244540.9610.25599.4
3.2-3.344.8110.1658.9820982438043610.9780.18599.6
3.34-3.515.3440.12911.9422162415041470.9890.14399.9
3.51-3.75.2840.10713.9520961397439670.990.11999.8
3.7-3.925.170.08516.4319346375037420.9930.09599.8
3.92-4.195.0660.07418.5917889353735310.9930.08299.8
4.19-4.534.8250.06519.9715953332333060.9940.07399.5
4.53-4.964.4490.05720.3213277302829840.9960.06598.5
4.96-5.555.1460.0621.9614311279027810.9960.06799.7
5.55-6.45.0780.0621.7112441245624500.9950.06799.8
6.4-7.844.8220.05323.3510145212121040.9950.0699.2
7.84-11.094.4170.04724.797174164316240.9960.05398.8
11.09-394.7950.04927.1944409719260.9960.05595.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model from the Chloro derivative

Resolution: 2.48→39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1826 / WRfactor Rwork: 0.1591 / FOM work R set: 0.8627 / SU B: 10.683 / SU ML: 0.127 / SU R Cruickshank DPI: 0.1736 / SU Rfree: 0.1542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 3768 4.9 %RANDOM
Rwork0.1676 ---
obs0.1688 72899 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.23 Å2 / Biso mean: 48.26 Å2 / Biso min: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å2-0 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.48→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 628 245 7315
Biso mean--56.84 50.18 -
Num. residues----819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176979
X-RAY DIFFRACTIONr_angle_refined_deg2.2191.70410077
X-RAY DIFFRACTIONr_angle_other_deg1.2181.61915974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.519.972353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70615964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5471531
X-RAY DIFFRACTIONr_chiral_restr0.0740.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028235
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021771
LS refinement shellResolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 281 -
Rwork0.264 5306 -
all-5587 -
obs--99.25 %
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)
11.02210.26550.09070.388-0.08180.74830.04670.06280.0436-0.042-0.0254-0.0413-0.11770.0918-0.02130.2059-0.06060.0380.0356-0.00110.015275.491-11.322-16.259
20.91130.1372-0.34390.2348-0.19390.79-0.0205-0.1831-0.17640.0448-0.0754-0.06420.0060.09280.0960.1973-0.06050.02870.06310.03430.046760.66-30.6590.711
30.4910.2675-0.1920.2843-0.24790.65130.0593-0.04190.1020.05520.01230.0987-0.0787-0.0614-0.07160.1822-0.0450.05510.0345-0.00550.047247.612-12.8112.415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H11 - 248
2X-RAY DIFFRACTION2L1 - 281
3X-RAY DIFFRACTION3M3 - 302

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