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- PDB-7mh9: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -

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Basic information

Entry
Database: PDB / ID: 7mh9
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-nitrotyrosine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / photosynthetic / membrane protein / noncanonical amino acid / nitrotyrosine
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, 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 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, 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 / 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: 3.1 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

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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)105,39820
Polymers94,9763
Non-polymers10,42217
Water2,432135
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 area36310 Å2
ΔGint-234 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.210, 141.210, 187.590
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-556-

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) / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34574.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: pIND4-RC-M210TAG-A7 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): RCx / References: UniProt: P0C0Y9

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Non-polymers , 9 types, 152 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: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 5.68 Å3/Da / Density % sol: 78.36 %
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: Feb 11, 2019
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: 3.1→39.07 Å / Num. obs: 39799 / % possible obs: 99.9 % / Redundancy: 16.62 % / Biso Wilson estimate: 52.089 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.347 / Rrim(I) all: 0.358 / Χ2: 0.843 / Net I/σ(I): 7.18 / Num. measured all: 661446 / Scaling rejects: 91
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
3.1-3.1817.051.5331.6349770291929190.7061.58100
3.18-3.2716.9691.3271.9448226284328420.7541.367100
3.27-3.3616.59512.6545670275527520.851.03299.9
3.36-3.4716.0190.7953.3342756266926690.9030.821100
3.47-3.5815.2990.7183.5939670259325930.9060.743100
3.58-3.7117.4960.6034.5544336253425340.9270.621100
3.71-3.8517.420.4845.642209242424230.9540.498100
3.85-417.2590.426.4340439234323430.9670.433100
4-4.1817.1740.3457.8538745225622560.9760.355100
4.18-4.3816.9540.3048.6236418214821480.9850.314100
4.38-4.6216.6830.2719.7834166204820480.9840.28100
4.62-4.916.1280.24310.3931805197219720.990.251100
4.9-5.2414.6630.259.7326804183118280.9860.25999.8
5.24-5.6617.3820.2729.8129706170917090.9850.28100
5.66-6.217.3340.2859.3727301157515750.9840.294100
6.2-6.9317.0560.22811.3724799145414540.9890.235100
6.93-816.5370.19812.6821134127912780.9920.20499.9
8-9.815.1430.12717.6916688110211020.9960.131100
9.8-13.8615.4070.10721.01134048708700.9980.11100
13.86-39.0715.2890.06727.2974005154840.9990.06994

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHLROTYROSINE MODEL

Resolution: 3.1→39.07 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.1913 / WRfactor Rwork: 0.1558 / FOM work R set: 0.852 / SU B: 21.901 / SU ML: 0.2 / SU R Cruickshank DPI: 0.4833 / SU Rfree: 0.2832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1990 5 %RANDOM
Rwork0.1694 ---
obs0.1711 37808 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.45 Å2 / Biso mean: 58.559 Å2 / Biso min: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å2-0 Å2
2--0.38 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: final / Resolution: 3.1→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 1355 137 7232
Biso mean--61.03 51.12 -
Num. residues----729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137365
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176994
X-RAY DIFFRACTIONr_angle_refined_deg2.2181.70510082
X-RAY DIFFRACTIONr_angle_other_deg1.1731.61916011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43620353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19515970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.861531
X-RAY DIFFRACTIONr_chiral_restr0.0610.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028224
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021766
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 144 -
Rwork0.275 2740 -
all-2884 -
obs--100 %
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)
10.2013-0.06230.03660.32580.03940.3330.0075-0.04150.04030.02190.01960.0325-0.07530.0583-0.02710.0613-0.04540.01640.0421-0.01630.0201-47.74159.68916.195
20.1043-0.063-0.07340.42340.16380.3034-0.01860.025-0.0048-0.0604-0.04030.1145-0.0455-0.00160.05890.0622-0.0434-0.01070.0505-0.01930.0387-56.7937.073-0.692
30.12470.11260.0830.43890.19060.416-0.00210.0373-0.02340.02540.0442-0.09470.01090.0667-0.04210.0319-0.03280.01170.0535-0.02880.0304-34.92634.852-2.416
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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