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- PDB-7mh5: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -

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Basic information

Entry
Database: PDB / ID: 7mh5
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-iodotyrosine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / photosynthetic / membrane protein / noncanonical amino acid / iodotyrosine
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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: 2.85 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

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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)105,56919
Polymers95,1823
Non-polymers10,38716
Water3,315184
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 area35360 Å2
ΔGint-227 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.414, 141.414, 186.502
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 34781.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TYI in parentheses is used to denote 3,5-diiodotyrosine
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: Plasmid / Details (production host): pIND4-RC-M210TAG-HaloY1 / Production host: Luteovulum sphaeroides (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 8 types, 200 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-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
#6: 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
#7: 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
#8: Chemical ChemComp-FE / FE (III) ION


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


Mass: 568.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C41H60O
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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

CrystalDensity Matthews: 5.66 Å3/Da / Density % sol: 78.25 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.85→38.95 Å / Num. obs: 50807 / % possible obs: 99.9 % / Redundancy: 6.711 % / Biso Wilson estimate: 72.806 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.126 / Χ2: 1.046 / Net I/σ(I): 12.18 / Num. measured all: 340963 / Scaling rejects: 3
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
2.85-2.926.9641.2871.6125803370537050.5821.391100
2.92-36.890.9952.1225059364036370.691.07799.9
3-3.096.8240.7992.6123883350035000.7710.865100
3.09-3.196.4680.623.2722191343534310.8350.67599.9
3.19-3.2960.444.2120083335033470.890.48299.9
3.29-3.417.2130.3226.3623032319331930.9610.347100
3.41-3.547.1640.2567.7522346311931190.9720.276100
3.54-3.687.1020.2039.6221115297429730.980.219100
3.68-3.847.0060.15112.3520344290429040.9880.163100
3.84-4.036.9170.12314.8319043275327530.9910.133100
4.03-4.256.8090.09917.4417854262226220.9940.107100
4.25-4.516.4860.08519.4416117248624850.9950.092100
4.51-4.825.7350.07320.0313408234523380.9950.0899.7
4.82-5.26.7960.07422.5614917219621950.9960.08100
5.2-5.76.8840.07322.7713919202220220.9960.079100
5.7-6.376.8080.06923.4312506183718370.9970.075100
6.37-7.366.4630.05726.6410587164116380.9970.06299.8
7.36-9.015.970.04628.468281139413870.9980.05199.5
9.01-12.756.0590.04133.146677110311020.9970.04599.9
12.75-38.956.1360.04135.2537986566190.9980.04594.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model from the Photosynthetic Reaction Center variant with Chlorotyrosine at M210

Resolution: 2.85→38.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.1802 / FOM work R set: 0.8754 / SU B: 17.596 / SU ML: 0.181 / SU R Cruickshank DPI: 0.3211 / SU Rfree: 0.2305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2495 4.9 %RANDOM
Rwork0.1802 ---
obs0.1814 48339 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.1 Å2 / Biso mean: 68.929 Å2 / Biso min: 31.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.85→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 617 184 7252
Biso mean--78.36 61.89 -
Num. residues----820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176971
X-RAY DIFFRACTIONr_angle_refined_deg2.2091.70410077
X-RAY DIFFRACTIONr_angle_other_deg1.1481.61915959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0975821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15220.057352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20815968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8321531
X-RAY DIFFRACTIONr_chiral_restr0.0670.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028232
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021770
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 178 -
Rwork0.283 3520 -
all-3698 -
obs--99.86 %
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)
11.52260.39840.24850.6677-0.18441.31140.09880.04050.0252-0.0202-0.104-0.0877-0.2680.20690.00520.3301-0.10650.0580.06970.00230.045875.79-11.305-16.174
21.42830.1306-0.40320.3906-0.22561.00860.0021-0.3179-0.3190.0936-0.1634-0.1054-0.01850.16120.16130.3279-0.14650.02950.16170.08780.13260.784-30.5260.741
30.72720.3598-0.28210.3285-0.35191.2260.0806-0.08060.20650.06860.01290.1057-0.1178-0.0985-0.09350.3327-0.11560.03050.0766-0.02510.130547.698-12.7722.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H11 - 249
2X-RAY DIFFRACTION2L1 - 281
3X-RAY DIFFRACTION3M3 - 302

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