[English] 日本語
Yorodumi
- PDB-8ivk: Cryogenic temperature crystal structure of Escherichia coli CyaY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ivk
TitleCryogenic temperature crystal structure of Escherichia coli CyaY
ComponentsIron-sulfur cluster assembly protein CyaY
KeywordsMETAL BINDING PROTEIN / CyaY / Escherichia coli / Frataxin
Function / homology
Function and homology information


iron chaperone activity / iron-sulfur cluster assembly / ferroxidase activity / ferric iron binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / cytosol
Similarity search - Function
: / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily
Similarity search - Domain/homology
Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShafiei, A. / DeMirci, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Cryogenic temperature crystal structure of Escherichia coli CyaY
Authors: Shafiei, A. / DeMirci, H.
History
DepositionMar 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron-sulfur cluster assembly protein CyaY


Theoretical massNumber of molelcules
Total (without water)12,2421
Polymers12,2421
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.456, 44.456, 98.425
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Iron-sulfur cluster assembly protein CyaY


Mass: 12242.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyaY / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C3SKF0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M Citric acid, 4.0 M Sodium chloride (pH 4.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→22.23 Å / Num. obs: 18719 / % possible obs: 99.89 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 14.11
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1821 / CC1/2: 0.582

-
Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
CrysalisPro1.171.42.35adata reduction
CrysalisPro1.171.42.35adata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.23 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1867 9.97 %
Rwork0.1764 --
obs0.1804 18718 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→22.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 0 159 1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019
X-RAY DIFFRACTIONf_angle_d1.482
X-RAY DIFFRACTIONf_dihedral_angle_d6.285120
X-RAY DIFFRACTIONf_chiral_restr0.099129
X-RAY DIFFRACTIONf_plane_restr0.017171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.24591430.24241289X-RAY DIFFRACTION99
1.54-1.590.26111360.21941257X-RAY DIFFRACTION100
1.59-1.640.25641420.20941271X-RAY DIFFRACTION100
1.64-1.70.25091390.20371252X-RAY DIFFRACTION100
1.7-1.760.21751370.18411293X-RAY DIFFRACTION100
1.76-1.840.24051430.17811286X-RAY DIFFRACTION100
1.84-1.940.17041400.17261287X-RAY DIFFRACTION100
1.94-2.060.20851400.16641271X-RAY DIFFRACTION100
2.06-2.220.20261470.15461306X-RAY DIFFRACTION100
2.22-2.440.19911420.17811292X-RAY DIFFRACTION100
2.45-2.80.19251480.18211314X-RAY DIFFRACTION100
2.8-3.520.22421510.16911319X-RAY DIFFRACTION100
3.52-22.230.22771590.16141414X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.76781.61623.55623.49422.47275.7280.01190.1553-0.08380.08950.0756-0.09960.05670.2548-0.11690.07420.00690.01420.05440.00630.1228-16.2375-4.2717-14.7896
21.74741.19891.01242.19231.24052.1250.1768-0.1114-0.12410.2826-0.0477-0.3130.10620.0558-0.09460.1011-0.0156-0.02150.07760.00290.0961-16.70466.363-1.3869
32.35591.58712.11564.72243.86295.96440.1305-0.0767-0.0444-0.1039-0.1025-0.090.0473-0.29680.05370.0809-0.0135-0.00470.08820.00210.0758-23.13695.0652-12.181
42.56890.21310.70083.3261.76744.93410.03510.2514-0.0365-0.15270.04440.0113-0.05150.0661-0.02480.06790.0063-0.01090.06890.00950.0713-21.48347.1784-19.6401
52.9644-0.31280.79733.81720.28166.3290.02310.5145-0.3398-0.2401-0.0959-0.54160.49710.4457-0.05490.11540.01830.05130.1613-0.01740.1857-12.82193.6777-23.7907
63.6148-0.56013.31033.6585-0.73023.4367-0.28390.2130.7127-0.19810.16370.1908-0.5568-0.19470.24680.1421-0.0231-0.01850.13630.04030.136-15.885912.3248-24.0598
72.14790.20630.34750.58852.04557.4863-0.01970.0030.0012-0.0827-0.026-0.1681-0.21040.1410.02570.0591-0.02170.00570.05430.01630.0754-11.480712.1366-11.2057
82.99240.5851.85442.740.48864.6091-0.0485-0.0324-0.35030.11490.2042-0.39250.48150.3613-0.1730.0934-0.01030.0170.13960.0030.148-5.45489.0103-7.3842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 80 )
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 86 )
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 99 )
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 106 )

+
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