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- PDB-9fy7: Dye Type Peroxidase Aa from Streptomyces lividans with N3 ligand ... -

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Basic information

Entry
Database: PDB / ID: 9fy7
TitleDye Type Peroxidase Aa from Streptomyces lividans with N3 ligand by serial electron diffraction (SerialED)
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / serial electron diffraction / SerialED / DPtAa / oxireductase / heme
Function / homologyAZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesStreptomyces lividans (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 1.1 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

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Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3976
Polymers80,0802
Non-polymers1,3174
Water15,799877
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-59 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.770, 67.400, 73.630
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

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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-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: PARTICLE / 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 (E. coli) / Strain: C43(DE3)
Buffer solutionpH: 7
SpecimenConc.: 30 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 / Calibrated defocus max: 0 nm / Cs: 0 mm / 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)
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
2.37-21.471197.552.52597215.53
1.1-1.142133.152.5865468.87
EM diffraction statsFourier space coverage: 79.62 % / High resolution: 1.1 Å / Num. of intensities measured: 250637 / Num. of structure factors: 220288 / Phase error: 35.84 ° / Phase error rejection criteria: 0 / Rmerge: 23

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Processing

EM software
IDNameCategory
9PHENIXmolecular replacement
13PHENIX3D reconstruction
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 correctionDetails: Diffraction experiment / Type: NONE
3D reconstructionResolution: 1.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Atomic model buildingPDB-ID: 6I43

6i43


Accession code: 6I43 / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→21.47 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 11000 4.99 %random selection
Rwork0.2161 ---
obs0.2172 220285 79.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.015850
ELECTRON CRYSTALLOGRAPHYf_angle_d0.9957962
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d14.8212101
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.079826
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0171060
LS refinement shell
Resolution (Å)Rfactor Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.140.43420.42968654ELECTRON CRYSTALLOGRAPHY33.1
2.37-21.470.16474.990.144325972ELECTRON CRYSTALLOGRAPHY97.5

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