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- PDB-9fyk: Dye Type Peroxidase Aa from Streptomyces lividans by serial elect... -

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Basic information

Entry
Database: PDB / ID: 9fyk
TitleDye Type Peroxidase Aa from Streptomyces lividans by serial electron diffraction (SerialED)
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / serial electron diffraction / SerialED / DPtAa / oxireductase / heme
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesStreptomyces lividans (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 1.3 Å
AuthorsHofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Finjallaz, A. / Williams, L. / Worral, J. / Steiner, R. / Xu, H. / Zou, X.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Universal Serial electron diffraction for high quality protein structures
Authors: Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Williams, L. / Worrall, J. / Steiner, R. / Xu, H. / Zou, X.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 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: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3134
Polymers80,0802
Non-polymers1,2332
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-60 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.770, 67.400, 73.630
Angle α, β, γ (deg.)90.000, 105.800, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Deferrochelatase / Peroxidase EfeB


Mass: 40039.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SSPG_05265 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: A0A7U8YY09, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Dye type peroxidase Aa / Type: COMPLEX / Details: Dye type peroxidase Aa from Streptomyces lividans / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 81.75 kDa/nm / Experimental value: NO
Source (natural)Organism: Streptomyces lividans (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C43
Buffer solutionpH: 7
Details: Crystals were produced by adding 3 parts of precipitation mix (25% PEG, 100 mM HEPES pH=7.0) to 2 parts of protein solution (31 g/L)
Buffer component
IDConc.NameBuffer-ID
125 %PEG1
2100 mMHEPES pH=7.01
SpecimenConc.: 31 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Crystall slurry produced from dye type peroxidase Aa
Specimen supportGrid material: COPPER / Grid type: C-flat-1/1
VitrificationCryogen name: ETHANE
Details: Manual blotting in room temperature with ambient humidity

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Calibrated defocus min: 0 nm / C2 aperture diameter: 20 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 78 K
Image recordingElectron dose: 3.5 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Details: FEI Ceta-D CMOS detector
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
2.8-19.341184.947.81376616.8
1.3-1.352172.347.81150248.34
EM diffraction statsFourier space coverage: 80.02 % / High resolution: 1.3 Å / Num. of intensities measured: 10379173 / Num. of structure factors: 134401 / Phase error rejection criteria: 0 / Rmerge: 25
ReflectionBiso Wilson estimate: 10.92 Å2

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Processing

EM software
IDNameCategory
8PHENIXmolecular replacement
12PHENIX3D reconstruction
13PHENIXmodel refinement
Image processingDetails: FEI Ceta-D CMOS detector
EM 3D crystal entity∠α: 90 ° / ∠β: 105.8 ° / ∠γ: 90 ° / A: 72.77 Å / B: 67.4 Å / C: 73.63 Å / Space group name: P1211 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution: 1.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 13.88 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: maximum-likelihood
Atomic model buildingPDB-ID: 6I43

6i43


Accession code: 6I43 / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→19.34 Å / SU ML: 0.2439 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 6711 4.99 %Random Selection
Rwork0.2123 127690 --
obs0.214 134401 80.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0135835
ELECTRON CRYSTALLOGRAPHYf_angle_d1.06747945
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0807826
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.01871057
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d10.946818
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.350.39146.210.38691150372.3
2.8-19.340.17917290.15241376684.9

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