[English] 日本語
Yorodumi
- PDB-7wgu: Crystal structure of metal-binding protein EfeO from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wgu
TitleCrystal structure of metal-binding protein EfeO from Escherichia coli
ComponentsIron uptake system protein EfeO
KeywordsMETAL BINDING PROTEIN / EfeO / Escherichia coli / Iron
Function / homology
Function and homology information


EfeO/Algp7, imelysin-like domain / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / EfeO-type cupredoxin-like domain / Cupredoxin-like domain / Cupredoxin
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Iron uptake system component EfeO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNakatsuji, S. / Takase, R. / Mikami, B. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of EfeB and EfeO in a bacterial siderophore-independent iron transport system
Authors: Nakatsuji, S. / Okumura, K. / Takase, R. / Watanabe, D. / Mikami, B. / Hashimoto, W.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron uptake system protein EfeO
B: Iron uptake system protein EfeO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,34836
Polymers79,1152
Non-polymers2,23334
Water5,801322
1
A: Iron uptake system protein EfeO
hetero molecules

B: Iron uptake system protein EfeO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,34836
Polymers79,1152
Non-polymers2,23334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544-x+1/2,y-1/2,-z-11
Buried area9670 Å2
ΔGint1 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.907, 51.877, 117.379
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Iron uptake system protein EfeO


Mass: 39557.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: efeO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7T2JMH3

-
Non-polymers , 6 types, 356 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.17 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 160 mM ammonium sulfate, 80 mM sodium acetate trihydrate (pH 4.6), 20% PEG 4000, 20% glycerol 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→48.15 Å / Num. obs: 65646 / % possible obs: 97.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.046 / Net I/σ(I): 18.5
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 9994 / CC1/2: 0.918 / Rrim(I) all: 0.469 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4C

5y4c


Resolution: 1.85→48.15 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 3279 5 %
Rwork0.1993 --
obs0.2015 65616 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 140 322 5839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065831
X-RAY DIFFRACTIONf_angle_d0.8177852
X-RAY DIFFRACTIONf_dihedral_angle_d15.4552221
X-RAY DIFFRACTIONf_chiral_restr0.048888
X-RAY DIFFRACTIONf_plane_restr0.0051027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.36851200.33972310X-RAY DIFFRACTION84
1.87-1.90.33551380.27712620X-RAY DIFFRACTION95
1.9-1.940.30291400.2492641X-RAY DIFFRACTION96
1.94-1.970.26811420.2332697X-RAY DIFFRACTION98
1.97-20.29331430.2322712X-RAY DIFFRACTION98
2-2.040.27631400.23562664X-RAY DIFFRACTION99
2.04-2.080.31851450.22522753X-RAY DIFFRACTION99
2.08-2.130.26921430.232714X-RAY DIFFRACTION99
2.13-2.180.24451410.20592698X-RAY DIFFRACTION99
2.18-2.230.27121430.21622733X-RAY DIFFRACTION99
2.23-2.290.25371440.21772722X-RAY DIFFRACTION99
2.29-2.360.30361430.21852727X-RAY DIFFRACTION99
2.36-2.440.27911440.22692736X-RAY DIFFRACTION99
2.44-2.530.29581420.22312710X-RAY DIFFRACTION99
2.53-2.630.26121450.22212753X-RAY DIFFRACTION99
2.63-2.750.28381440.21862748X-RAY DIFFRACTION99
2.75-2.890.23371460.20722758X-RAY DIFFRACTION99
2.89-3.070.23271440.20182745X-RAY DIFFRACTION99
3.07-3.310.26731430.20242713X-RAY DIFFRACTION98
3.31-3.640.22321440.1892738X-RAY DIFFRACTION98
3.64-4.170.19971460.1712783X-RAY DIFFRACTION99
4.17-5.250.20491490.16032815X-RAY DIFFRACTION99
5.26-48.150.22481500.18482847X-RAY DIFFRACTION98

+
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