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- PDB-8d9p: De Novo Photosynthetic Reaction Center Protein Equipped with Heme... -

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Basic information

Entry
Database: PDB / ID: 8d9p
TitleDe Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) cations
ComponentsReaction center maquette
KeywordsDE NOVO PROTEIN / maquette / protein design / charge separation / artificial photosynthesis
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)23,2925
Polymers22,5301
Non-polymers7624
Water1,47782
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)44.968, 44.968, 238.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.68 Å3/Da / Density % sol: 54.11 % / Description: octahedral
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 1.2 M Li2SO4, 0.5 M (NH4)2SO4, 150 mM Na citrate, pH 5.9 Cryoprotectant: 28% glycerol, 1.25 M Li2SO4, 0.5 M (NH4)2SO4, 100 mM Na citrate, pH 5.85

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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: Sep 23, 2014 / 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: 1.9→23.25 Å / Num. obs: 20059 / % possible obs: 98.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.093 / Net I/σ(I): 22.22
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.66 / Num. unique obs: 1271 / CC1/2: 0.619 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEVERSION January 10, 2014 BUILT=20140307data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VJS

5vjs


Resolution: 1.9→23.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.475 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.16 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24336 1014 5.1 %RANDOM
Rwork0.2189 ---
obs0.22014 19019 98.26 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.956 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 46 82 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0181656
X-RAY DIFFRACTIONr_bond_other_d0.0010.021637
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.9622212
X-RAY DIFFRACTIONr_angle_other_deg0.9762.8443770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5545194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29826.18697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93115348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.474157
X-RAY DIFFRACTIONr_chiral_restr0.0450.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021913
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02369
X-RAY DIFFRACTIONr_mcbond_it9.3793.052779
X-RAY DIFFRACTIONr_mcbond_other9.3343.04777
X-RAY DIFFRACTIONr_mcangle_it10.6714.544972
X-RAY DIFFRACTIONr_mcangle_other10.6774.545972
X-RAY DIFFRACTIONr_scbond_it18.4594.263877
X-RAY DIFFRACTIONr_scbond_other18.3774.254875
X-RAY DIFFRACTIONr_scangle_other20.3465.8011240
X-RAY DIFFRACTIONr_long_range_B_refined19.62837.6051916
X-RAY DIFFRACTIONr_long_range_B_other19.7237.4731903
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 63 -
Rwork0.37 1190 -
obs--85.53 %

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