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- PDB-7wgu: Crystal structure of metal-binding protein EfeO from Escherichia coli -

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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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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Non-polymers , 6 types, 356 molecules

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


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


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


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


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


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

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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