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- PDB-7unj: De novo designed chlorophyll dimer protein with Zn pheophorbide a... -

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Basic information

Entry
Database: PDB / ID: 7unj
TitleDe novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester matching geometry of purple bacterial special pair, SP1-ZnPPaM
ComponentsSP1-ZnPPaM designed chlorophyll dimer protein
KeywordsDE NOVO PROTEIN / design / homodimer / rosetta / symmetric / designed / circular tandem repeat protein / cTRP / apo / chlorophyll
Function / homologyChem-OE9
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKennedy, M.A. / Stoddard, B.L. / Ennist, N.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1762114 United States
Advanced Research Projects Agency-Energy (ARPA-E)DE-AR0001543 United States
Audacious Project at the Institute for Protein Design68-2492: Audacious GC5: Next-Generation Nanoengineering United States
CitationJournal: Nat Chem Biol / Year: 2024
Title: De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh ...Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh Hua / Arundhati P Deshmukh / Adam P Moyer / Derrick R Hicks / Avi Z Swartz / Ralph A Cacho / Nathan Novy / Asim K Bera / Alex Kang / Banumathi Sankaran / Matthew P Johnson / Amala Phadkule / Mike Reppert / Damian Ekiert / Gira Bhabha / Lance Stewart / Justin R Caram / Barry L Stoddard / Elisabet Romero / C Neil Hunter / David Baker /
Abstract: Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer ...Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
History
DepositionApr 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: 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 1.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SP1-ZnPPaM designed chlorophyll dimer protein
B: SP1-ZnPPaM designed chlorophyll dimer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2858
Polymers49,6632
Non-polymers1,6226
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, size exclusion chromatography (SEC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-37 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.349, 52.349, 173.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein SP1-ZnPPaM designed chlorophyll dimer protein


Mass: 24831.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-OE9 / [methyl 9-ethenyl-14-ethyl-3-(3-methoxy-3-oxopropyl)-4,8,13,18-tetramethyl-20-oxophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc


Mass: 670.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H36N4O5Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 3350, 200mM Lithium sulfate, 100mM BisTris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31457 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Χ2: 0.886 / Net I/σ(I): 13.9 / Num. measured all: 409604
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0713.20.42931200.9670.1210.4460.51199.7
2.07-2.1513.20.28931230.9830.0820.30.57699.9
2.15-2.2512.70.23331680.9880.0670.2420.92599.9
2.25-2.3713.70.16331200.9950.0450.1690.847100
2.37-2.5213.80.11831470.9970.0330.1230.941100
2.52-2.7113.10.10631490.9960.0310.1111.04100
2.71-2.9913.50.08831330.9980.0250.0911.043100
2.99-3.42130.07231460.9980.0210.0751.089100
3.42-4.3112.30.05831700.9980.0170.061.01299.7
4.31-5011.80.0531810.9990.0150.0520.87699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å38.83 Å
Translation2 Å38.83 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.8.3phasing
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: computationally generated

Resolution: 2→38.83 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2003 6.38 %
Rwork0.1912 29373 -
obs0.1939 31376 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.66 Å2 / Biso mean: 45.3089 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 2→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 107 63 3373
Biso mean--46.03 46.14 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.26231370.21112067220499
2.05-2.10.29661480.218720962244100
2.1-2.170.27051410.214621182259100
2.17-2.240.30491440.222220822226100
2.24-2.320.29461390.217820712210100
2.32-2.410.24071450.196221102255100
2.41-2.520.24731420.188921142256100
2.52-2.650.21581370.196320982235100
2.65-2.820.30121460.211721122258100
2.82-3.040.23751400.239120962236100
3.04-3.340.24741460.222120882234100
3.34-3.820.23061430.185921012244100
3.82-4.820.20351400.156221132253100
4.82-38.830.20141550.17212107226299
Refinement TLS params.Method: refined / Origin x: 23.7177 Å / Origin y: -2.2259 Å / Origin z: -0.6216 Å
111213212223313233
T0.2059 Å2-0.0365 Å20.031 Å2-0.2126 Å2-0.0306 Å2--0.242 Å2
L0.7268 °2-0.2252 °2-0.1585 °2-0.8084 °20.2187 °2--0.9976 °2
S0.0128 Å °0.0249 Å °-0.0281 Å °-0.0117 Å °-0.0003 Å °0.042 Å °-0.0833 Å °0.0684 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 218
2X-RAY DIFFRACTION1allB2 - 218
3X-RAY DIFFRACTION1allD1 - 2
4X-RAY DIFFRACTION1allC1 - 82
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1 - 3

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