[English] 日本語
Yorodumi
- PDB-9fyh: Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fyh
TitleDye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / microcrystal electron diffraction / MicroED / 3D ED / DPtAa / oxireductase / heme
Function / homology
Function and homology information


iron import into cell / cell envelope / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / lyase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
Deferrochelatase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7134
Polymers80,4802
Non-polymers1,2332
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-61 kcal/mol
Surface area27300 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

-
Components

#1: Protein Deferrochelatase


Mass: 40240.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A7U9DT46
#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.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Dye type peroxidase Aa / Type: COMPLEX / Details: Dye type peroxidase Aa from Streptomyces lividans / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.08175 MDa / 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 mMHEPES1
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 type: C-flat-1/1
VitrificationCryogen name: ETHANE
Details: Manual blotting in room temperature with ambient humidity

-
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 / 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 recordingAverage exposure time: 1 sec. / Electron dose: 0.115 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Details: FEI Ceta-D CMOS detector
EM imaging opticsPhase plate: OTHER / Spherical aberration corrector: Diffraction experiment
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
6.54-19.461189.710211520.43
2.4-2.442176.28.1175329.72
EM diffraction statsFourier space coverage: 87.76 % / High resolution: 2.4 Å / Num. of intensities measured: 23722 / Num. of structure factors: 23683 / Phase error rejection criteria: 0 / Rmerge: 55.3
ReflectionBiso Wilson estimate: 23.3 Å2

-
Processing

EM software
IDNameCategory
6PHENIXmodel fitting
8PHENIXmolecular replacement
11PHENIXcrystallography merging
12PHENIX3D reconstruction
13PHENIXmodel refinement
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: 2.4 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 18.52 / 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: 2.4→19.46 Å / SU ML: 0.3515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 2962 6.42 %Random selection
Rwork0.2019 43153 --
obs0.2053 46115 87.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00255840
ELECTRON CRYSTALLOGRAPHYf_angle_d0.55717952
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0388827
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00491058
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d9.3745819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.30551370.26651753ELECTRON CRYSTALLOGRAPHY76.18
2.44-2.480.3485940.26241852ELECTRON CRYSTALLOGRAPHY76.7
2.48-2.530.2971170.26411810ELECTRON CRYSTALLOGRAPHY77.76
2.53-2.570.36141490.26612044ELECTRON CRYSTALLOGRAPHY88.71
2.57-2.630.33041450.25862098ELECTRON CRYSTALLOGRAPHY88.1
2.63-2.680.31361540.27062122ELECTRON CRYSTALLOGRAPHY90.39
2.68-2.750.29551290.25682065ELECTRON CRYSTALLOGRAPHY88.54
2.75-2.810.32291160.2462099ELECTRON CRYSTALLOGRAPHY88.92
2.81-2.890.3221620.24932079ELECTRON CRYSTALLOGRAPHY90.84
2.89-2.980.32311500.25032098ELECTRON CRYSTALLOGRAPHY89.45
2.98-3.070.30641420.2322139ELECTRON CRYSTALLOGRAPHY89.59
3.07-3.180.30091610.2272102ELECTRON CRYSTALLOGRAPHY90.38
3.18-3.310.28041390.20972104ELECTRON CRYSTALLOGRAPHY89.86
3.31-3.460.23981260.18982127ELECTRON CRYSTALLOGRAPHY90.19
3.46-3.640.26581450.16982090ELECTRON CRYSTALLOGRAPHY89.26
3.64-3.860.18841650.16422071ELECTRON CRYSTALLOGRAPHY89.76
3.86-4.160.21181520.14882108ELECTRON CRYSTALLOGRAPHY90
4.16-4.570.17851440.14212100ELECTRON CRYSTALLOGRAPHY89.62
4.57-5.220.18591470.14462094ELECTRON CRYSTALLOGRAPHY89.35
5.22-6.540.2281450.18572083ELECTRON CRYSTALLOGRAPHY89.98
6.54-19.460.23691430.2032115ELECTRON CRYSTALLOGRAPHY89.67

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more