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- PDB-7mh3: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -

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Basic information

Entry
Database: PDB / ID: 7mh3
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-chlorotyrosine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / photosynthetic / membrane protein / noncanonical amino acid / chlorotyrosine
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 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 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 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 / Alpha Beta
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: 2.3 Å
AuthorsMathews, I. / Weaver, J.B. / 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 1.1Oct 18, 2023Group: 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

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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)105,42220
Polymers94,9993
Non-polymers10,42217
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Coordinate represent a complete multimer representing the biologically significant oligomerization state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35840 Å2
ΔGint-235 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.674, 141.674, 187.419
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-513-

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 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 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 center M subunit


Mass: 34598.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2LT in parentheses is used to denote 3,5-dichlorotyrosine
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, 329 molecules

#4: 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
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 312 / 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: 0.97893 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.3→39.11 Å / Num. obs: 91797 / % possible obs: 94.8 % / Redundancy: 5.276 % / Biso Wilson estimate: 54.371 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.127 / Χ2: 1.04 / Net I/σ(I): 9.8 / Num. measured all: 484297 / Scaling rejects: 2
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
2.3-2.365.1991.1871.5735620714868510.5531.31795.8
2.36-2.425.2440.9662.0434151685165120.6511.0795.1
2.42-2.495.1960.8472.3530710671959100.7160.9488
2.49-2.575.360.7262.933577655362640.8040.80295.6
2.57-2.665.410.5713.6833622634962150.8530.63197.9
2.66-2.755.4190.4844.3432131608259290.90.53497.5
2.75-2.855.3880.385.3331352597258190.9390.41997.4
2.85-2.975.3850.296.6329769572955280.9540.32196.5
2.97-3.15.380.2298.0527780543451640.9710.25395
3.1-3.255.1710.179.8624025527146460.980.18988.1
3.25-3.435.3980.12512.8725946496548070.9890.13896.8
3.43-3.645.4040.10215.1925258477646740.9920.11297.9
3.64-3.895.2830.08117.8922882444943310.9930.0997.3
3.89-4.25.2270.0720.1120944417640070.9940.07796
4.2-4.65.0380.06321.4517987384735700.9950.0792.8
4.6-5.144.9560.05922.3415468346231210.9940.06690.2
5.14-5.945.2230.0622.9215727311830110.9950.06696.6
5.94-7.275.1570.05723.5612749263224720.9960.06393.9
7.27-10.294.9990.05225.159078209418160.9960.05786.7
10.29-39.114.8010.05426.15521120411500.9940.0695.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j8c

2j8c


Resolution: 2.3→39.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1737 / WRfactor Rwork: 0.1543 / FOM work R set: 0.8726 / SU B: 7.821 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1355 / SU Rfree: 0.1218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 4508 4.9 %RANDOM
Rwork0.1571 ---
obs0.1579 86659 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.59 Å2 / Biso mean: 45.21 Å2 / Biso min: 24.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 2.3→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 628 313 7407
Biso mean--54.37 54.25 -
Num. residues----822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137387
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177006
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.70410122
X-RAY DIFFRACTIONr_angle_other_deg1.2121.61916041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.93920.028355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74315972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9221531
X-RAY DIFFRACTIONr_chiral_restr0.0720.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021776
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 329 -
Rwork0.251 6103 -
all-6432 -
obs--90.52 %
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)
10.6739-0.1789-0.03240.48840.05420.55780.0301-0.10090.04950.05960.02060.0794-0.089-0.0673-0.05070.18650.06320.04030.04450.00380.030365.975-11.5247.366
20.66-0.161-0.27510.1330.14690.4429-0.00570.1187-0.1283-0.0006-0.02790.0532-0.008-0.0610.03360.20420.04980.03690.0415-0.01920.048380.98-30.82130.521
30.2785-0.186-0.12490.36030.19590.4430.0468-0.01540.0765-0.04870.0399-0.1038-0.06630.0499-0.08670.18220.04060.06970.0265-0.01030.074193.945-13.01828.801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H11 - 250
2X-RAY DIFFRACTION2L1 - 281
3X-RAY DIFFRACTION3M2 - 302

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