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- PDB-9l08: Cyclic Trimer of Helix-Linked Cytochrome c555 -

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Basic information

Entry
Database: PDB / ID: 9l08
TitleCyclic Trimer of Helix-Linked Cytochrome c555
ComponentsCovalently Connected Cytochrome c555 trimer
KeywordsELECTRON TRANSPORT / cyclic protein / cytochrome c / electron transfer / heme protein / sortase A-mediated ligation / nanoporous structure
Function / homologyACETIC ACID / HEME C / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNovientri, G. / Mashima, T. / Matsuura, H. / Ogata, H. / Hirota, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K21152 Japan
Japan Science and TechnologyJP20338388 Japan
CitationJournal: Chemistry / Year: 2025
Title: Construction of a Cyclic Regular-Triangle Trimer of Cytochrome c 555 with a Central Hole Using Sortase A.
Authors: Novientri, G. / Fujiwara, K. / Mashima, T. / Matsuura, H. / Ogata, H. / Uchihashi, T. / Fujii, S. / Sambongi, Y. / Hirota, S.
History
DepositionDec 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Covalently Connected Cytochrome c555 trimer
B: Covalently Connected Cytochrome c555 trimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,00623
Polymers62,2082
Non-polymers4,79821
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.704, 104.519, 73.705
Angle α, β, γ (deg.)90.000, 92.953, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Covalently Connected Cytochrome c555 trimer


Mass: 31104.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 774 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200 mM lithium sulfate, 20% (w/v) PEG 8000, 200 mM sodium acetate buffer, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 112336 / % possible obs: 98.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 17.9
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 17912 / CC1/2: 0.801 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.12 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 5567 5 %
Rwork0.1717 105798 -
obs0.1737 111365 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 326 753 5429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615047
X-RAY DIFFRACTIONf_angle_d0.80446880
X-RAY DIFFRACTIONf_chiral_restr0.0408699
X-RAY DIFFRACTIONf_plane_restr0.0042899
X-RAY DIFFRACTIONf_dihedral_angle_d19.64841902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28861830.26473474X-RAY DIFFRACTION98.17
1.62-1.640.31961860.24313549X-RAY DIFFRACTION97.83
1.64-1.660.28221820.22853452X-RAY DIFFRACTION98.19
1.66-1.680.24521860.20563529X-RAY DIFFRACTION98.12
1.68-1.70.25041830.19183482X-RAY DIFFRACTION98.26
1.7-1.720.26331860.19963526X-RAY DIFFRACTION98.18
1.72-1.750.25371840.17323489X-RAY DIFFRACTION98.26
1.75-1.770.22821850.16143526X-RAY DIFFRACTION98.38
1.77-1.80.21451870.16033556X-RAY DIFFRACTION98.89
1.8-1.830.18381860.17113538X-RAY DIFFRACTION99.12
1.83-1.860.23861840.19993492X-RAY DIFFRACTION99
1.86-1.90.26361790.20493405X-RAY DIFFRACTION94.14
1.9-1.930.27281650.26013160X-RAY DIFFRACTION88.64
1.93-1.970.22871840.20673515X-RAY DIFFRACTION98.09
1.97-2.020.21261860.16263540X-RAY DIFFRACTION99.41
2.02-2.060.20981870.16773547X-RAY DIFFRACTION99.23
2.06-2.110.21711850.1753512X-RAY DIFFRACTION98.69
2.11-2.170.1991880.15523576X-RAY DIFFRACTION99.47
2.17-2.240.19171880.16323565X-RAY DIFFRACTION99.36
2.24-2.310.23161850.16743514X-RAY DIFFRACTION98.56
2.31-2.390.2231870.15863566X-RAY DIFFRACTION99.71
2.39-2.490.20321900.16323594X-RAY DIFFRACTION99.82
2.49-2.60.21981870.16173556X-RAY DIFFRACTION99.87
2.6-2.740.20321880.16383580X-RAY DIFFRACTION99.5
2.74-2.910.22181890.17173582X-RAY DIFFRACTION99.92
2.91-3.130.22871880.17343584X-RAY DIFFRACTION99.92
3.13-3.450.2041900.17123597X-RAY DIFFRACTION99.92
3.45-3.940.1791880.15533583X-RAY DIFFRACTION99.52
3.95-4.970.18141910.15173627X-RAY DIFFRACTION99.79
4.97-46.120.19781900.17683582X-RAY DIFFRACTION97.75

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