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- PDB-7mh8: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -

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Basic information

Entry
Database: PDB / ID: 7mh8
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-methyltyrosine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / photosynthetic / membrane protein / noncanonical amino acid / methyltyrosine
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 / 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: 2.75 Å
AuthorsMathews, I. / Weaver, J. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)105,33219
Polymers94,9453
Non-polymers10,38716
Water2,378132
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 area35820 Å2
ΔGint-230 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.960, 140.960, 187.010
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: 34543.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZDJ in parenthesis is Methyl Tyrosine / 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 , 8 types, 148 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 natural 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 natural 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 natural source / Formula: C59H90O4 / 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.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 5.65 Å3/Da / Density % sol: 78.23 %
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2018
Details: Rh coated collimating mirror, Toroidal focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.75→38.96 Å / Num. obs: 56220 / % possible obs: 99.7 % / Redundancy: 8.526 % / Biso Wilson estimate: 63.009 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.16 / Χ2: 1.027 / Net I/σ(I): 11.39 / Num. measured all: 479326 / Scaling rejects: 26
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
2.75-2.828.7431.4221.6736353415841580.6491.512100
2.82-2.98.6261.1642.0134280397839740.7021.2499.9
2.9-2.988.3980.9692.3732871391439140.7581.034100
2.98-3.077.7720.7722.8729341379437750.7940.82899.5
3.07-3.188.7890.633.7932159365936590.8710.67100
3.18-3.299.0290.5014.7932503360036000.9190.532100
3.29-3.418.9720.3466.6130791343234320.9580.368100
3.41-3.558.8640.2777.9429420331933190.970.295100
3.55-3.718.8040.2159.9928324321732170.9790.229100
3.71-3.898.6510.16412.3926177302730260.9870.175100
3.89-4.18.4190.13114.9124441290829030.990.1499.8
4.1-4.358.0190.10516.9821995276027430.9930.11399.4
4.35-4.657.8080.08919.2619903258725490.9940.09698.5
4.65-5.028.7810.07922.6721400243924370.9960.08499.9
5.02-5.58.7310.08421.7319471223122300.9960.089100
5.5-6.158.6570.08521.1917886206620660.9960.091100
6.15-7.18.3960.06824.7714987178617850.9970.07399.9
7.1-8.77.5240.05328.4511557155315360.9970.05798.9
8.7-12.38.2750.03740.9610029122412120.9990.0499
12.3-38.967.9390.0346.08543871968510.03295.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chloro coordiante

Resolution: 2.75→38.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1843 / WRfactor Rwork: 0.161 / FOM work R set: 0.8311 / SU B: 16.938 / SU ML: 0.172 / SU R Cruickshank DPI: 0.2716 / SU Rfree: 0.2073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2811 5 %RANDOM
Rwork0.1788 ---
obs0.1799 53409 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.65 Å2 / Biso mean: 61.351 Å2 / Biso min: 26.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å2-0 Å2
3----1.8 Å2
Refinement stepCycle: final / Resolution: 2.75→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6459 0 627 135 7221
Biso mean--71.92 56.68 -
Num. residues----821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137348
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176983
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.70410063
X-RAY DIFFRACTIONr_angle_other_deg1.1371.6215983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51620353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10715967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0961531
X-RAY DIFFRACTIONr_chiral_restr0.0620.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021766
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 206 -
Rwork0.298 3925 -
all-4131 -
obs--99.95 %
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)
10.43620.19880.0160.37160.08920.4381-0.0115-0.0491-0.02540.06450.03120.0653-0.0145-0.1148-0.01970.0210.02830.02150.13040.04260.0367-27.893-71.041-14.961
20.33160.2633-0.15070.4734-0.23120.3515-0.090.0245-0.1316-0.078-0.0036-0.11150.0449-0.03930.09350.03570.02860.0460.11820.01710.0655-3.693-67.553-31.785
30.41460.1322-0.20840.1645-0.01520.47860.05410.02130.0897-0.0055-0.00930.0391-0.0856-0.0432-0.04480.03040.04430.02260.10380.03840.062-12.756-47.533-33.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H11 - 249
2X-RAY DIFFRACTION2L1 - 281
3X-RAY DIFFRACTION3M2 - 302

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