[English] 日本語
Yorodumi
- PDB-6i7c: Dye type peroxidase Aa from Streptomyces lividans: imidazole complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i7c
TitleDye type peroxidase Aa from Streptomyces lividans: imidazole complex
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / imidazole / Peroxidase
Function / homology
Function and homology information


iron import into cell / ferrochelatase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase 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 / IMIDAZOLE / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMoreno-Chicano, T. / Ebrahim, A.E. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Duyvesteyn, H.
CitationJournal: Iucrj / Year: 2019
Title: High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.
Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / ...Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / Tono, K. / Worrall, J.A.R. / Owen, R.L. / Hough, M.A.
History
DepositionNov 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deferrochelatase/peroxidase
B: Deferrochelatase/peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0576
Polymers78,6862
Non-polymers1,3714
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-51 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.480, 68.030, 73.530
Angle α, β, γ (deg.)90.000, 105.570, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Deferrochelatase/peroxidase


Mass: 39343.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO2276 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RKQ2, 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: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7
Details: 1:1 ratio of a 6.5 mg/ml DtpAa protein solution with precipitant solution containing 20% PEG 6000, 100 mM HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.88→37 Å / Num. obs: 56220 / % possible obs: 100 % / Redundancy: 102 % / CC1/2: 0.96 / R split: 0.158 / Rmerge(I) obs: 0.224 / Net I/σ(I): 5.7
Reflection shellResolution: 1.88→1.93 Å / Mean I/σ(I) obs: 1.54 / CC1/2: 0.6 / R split: 0.639 / % possible all: 100
Serial crystallography measurementCollection time total: 80 hours / Focal spot size: 1.66 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / Pulse photon energy: 10.01 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Silicon nitride chip / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Mylar film / Sample solvent: Mother liquor

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5map

5map


Resolution: 1.88→35.295 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.45
Details: Data file deposited extends to higher resolution. The resolution limit was set in refinement
RfactorNum. reflection% reflection
Rfree0.1766 2830 5.04 %
Rwork0.1385 --
obs0.1404 56150 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.62 Å2 / Biso mean: 30.8175 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 1.88→35.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 165 414 6046
Biso mean--24.5 34.38 -
Num. residues----725
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.88-1.91240.29621380.289726442782
1.9124-1.94720.29531420.212126422784
1.9472-1.98460.2281540.186626452799
1.9846-2.02510.22381220.180926662788
2.0251-2.06920.22361410.171926602801
2.0692-2.11730.20261650.15526152780
2.1173-2.17020.20261470.1426532800
2.1702-2.22890.19481290.13326652794
2.2289-2.29450.17771430.138226442787
2.2945-2.36850.18221260.135926932819
2.3685-2.45320.17521320.135926702802
2.4532-2.55140.18031520.133626342786
2.5514-2.66740.21261370.138726662803
2.6674-2.8080.16841320.138926792811
2.808-2.98390.19121490.139926512800
2.9839-3.21410.18431520.141226832835
3.2141-3.53730.15431640.131126512815
3.5373-4.04850.16241230.111226982821
4.0485-5.09820.13441370.112726992836
5.0982-35.30090.15431450.151227622907

+
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://pdbjlvh1.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