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- PDB-8d9o: De Novo Photosynthetic Reaction Center Protein in Apo-State -

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Basic information

Entry
Database: PDB / ID: 8d9o
TitleDe Novo Photosynthetic Reaction Center Protein in Apo-State
ComponentsReaction Center Maquette
KeywordsDE NOVO PROTEIN / maquette / protein design / charge separation / artificial photosynthesis
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsEnnist, N.M. / Stayrook, S.E. / Dutton, P.L. / Moser, C.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DESC0001035 United States
Citation
Journal: Front Mol Biosci / Year: 2022
Title: Rational design of photosynthetic reaction center protein maquettes.
Authors: Ennist, N.M. / Stayrook, S.E. / Dutton, P.L. / Moser, C.C.
#1: Journal: To Be Published
Title: De Novo Protein Design of Photochemical Reaction Centers
Authors: Ennist, N.M. / Zhao, Z. / Stayrook, S.E. / Discher, B.M. / Dutton, P.L. / Moser, C.C.
History
DepositionJun 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 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
A: Reaction Center Maquette
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,76712
Polymers22,5301
Non-polymers1,23711
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.692, 23.693, 72.756
Angle α, β, γ (deg.)90.000, 99.930, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-207-

CD

21A-333-

HOH

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Components

#1: Protein Reaction Center Maquette


Mass: 22530.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.7 Å3/Da / Density % sol: 27.76 % / Description: Parallelepiped
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 24% w/v PEG1500, 100 mM CdCl2, 100 mM Na acetate, pH 4.8. Cryoprotectant: 2-methyl-2.4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 6, 2013 / Details: Osmic VariMax mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→18.46 Å / Num. obs: 14128 / % possible obs: 95.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.72 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.12
Reflection shellResolution: 1.783→1.829 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.79 / Num. unique obs: 737 / CC1/2: 0.95 / % possible all: 68.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEVERSION July 4, 2012 BUILT=20130706data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VJS

5vjs


Resolution: 1.78→18.46 Å / SU ML: 0.167 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 722 5.11 %RANDOM
Rwork0.1828 13405 --
obs0.1841 14127 95.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.34 Å2
Refinement stepCycle: LAST / Resolution: 1.78→18.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 11 95 1678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01371585
X-RAY DIFFRACTIONf_angle_d1.78192117
X-RAY DIFFRACTIONf_chiral_restr0.0817228
X-RAY DIFFRACTIONf_plane_restr0.0084286
X-RAY DIFFRACTIONf_dihedral_angle_d20.7003646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.920.23591250.20882331X-RAY DIFFRACTION84.37
1.92-2.110.21631550.17492697X-RAY DIFFRACTION96.71
2.11-2.420.19791530.15422712X-RAY DIFFRACTION97.88
2.42-3.040.21121360.18332777X-RAY DIFFRACTION98.08
3.05-18.460.20431530.19132888X-RAY DIFFRACTION98.64

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