[English] 日本語
Yorodumi
- PDB-9epj: DtpAa Y389F 41 fs 10 microjoules XFEL Pulse Data Collection -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9epj
TitleDtpAa Y389F 41 fs 10 microjoules XFEL Pulse Data Collection
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / peroxidase / 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)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWilliams, L.J. / Owen, R.L. / Worrall, J.A.R. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light SourceSTU0436 United Kingdom
CitationJournal: To Be Published
Title: DtpAa Y389F 41 fs 10 microjoules XFEL Pulse Data Collection
Authors: Williams, L.J. / Owen, R.L. / Worrall, J.A.R. / Hough, M.A.
History
DepositionMar 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 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
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-62 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 68.200, 74.600
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number4
Space group name H-MP1211

-
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) / 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: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 298 K / Method: batch mode / Details: 12% v/v PEG 3350, 100 mM HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 294.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.03 Å
DetectorType: PSI JUNGFRAU 8M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.38→34.12 Å / Num. obs: 147332 / % possible obs: 100 % / Redundancy: 115.7 % / CC1/2: 0.917 / Net I/σ(I): 4.05
Reflection shellResolution: 1.38→1.41 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 7322 / CC1/2: 0.376 / % possible all: 100
Serial crystallography measurementPulse duration: 36 fsec. / Pulse energy: 10 µJ
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
CrystFELdata scaling
CrystFELdata reduction
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→34.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.235 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19423 7127 4.9 %RANDOM
Rwork0.17042 ---
obs0.17159 137006 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.05 Å2
2---0.33 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.38→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 86 535 6165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125816
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165409
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.8497923
X-RAY DIFFRACTIONr_angle_other_deg0.6191.78812392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79710876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027219
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6751.6722904
X-RAY DIFFRACTIONr_mcbond_other1.6731.6712903
X-RAY DIFFRACTIONr_mcangle_it2.44733629
X-RAY DIFFRACTIONr_mcangle_other2.44833630
X-RAY DIFFRACTIONr_scbond_it3.022.012912
X-RAY DIFFRACTIONr_scbond_other3.0212.012910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6883.5034289
X-RAY DIFFRACTIONr_long_range_B_refined5.78817.676445
X-RAY DIFFRACTIONr_long_range_B_other5.73917.436394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 526 -
Rwork0.368 10094 -
obs--99.99 %

+
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