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- PDB-7oyi: Escherichia coli YtfE_E159L(MN) -

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Basic information

Entry
Database: PDB / ID: 7oyi
TitleEscherichia coli YtfE_E159L(MN)
ComponentsIron-sulfur cluster repair protein YtfE
KeywordsMETAL BINDING PROTEIN / di-iron
Function / homology
Function and homology information


response to nitrosative stress / protein repair / nitrite reductase activity / response to oxidative stress / iron ion binding / cytosol
Similarity search - Function
Iron-sulfur cluster repair protein YftE / Repair of iron centres family / Domain of Unknown function (DUF542) / Hemerythrin-like / Hemerythrin HHE cation binding domain
Similarity search - Domain/homology
: / OXYGEN ATOM / Iron-sulfur cluster repair protein YtfE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSilva, L.S.O. / Matias, P. / Romao, C.V. / Saraiva, L.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaSFRH/BD/118545/2016 Portugal
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: Molecules / Year: 2022
Title: Repair of Iron Center Proteins-A Different Class of Hemerythrin-like Proteins.
Authors: Silva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, L.M.
History
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-sulfur cluster repair protein YtfE
B: Iron-sulfur cluster repair protein YtfE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,88411
Polymers49,4092
Non-polymers4759
Water4,071226
1
A: Iron-sulfur cluster repair protein YtfE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0547
Polymers24,7041
Non-polymers3496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron-sulfur cluster repair protein YtfE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8304
Polymers24,7041
Non-polymers1263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.824, 49.671, 88.091
Angle α, β, γ (deg.)90.000, 100.481, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 5 or resid 7...
d_2ens_1(chain "B" and (resid 2 through 5 or resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAASPA1 - 4
d_12ens_1PROALAA6 - 72
d_13ens_1ILEILEA74 - 79
d_14ens_1ARGLEUA81 - 200
d_15ens_1ASPGLUA202 - 219
d_16ens_1MNMNB
d_17ens_1MNMNC
d_21ens_1ALAASPF1 - 4
d_22ens_1PROALAF6 - 72
d_23ens_1ILEILEF74 - 79
d_24ens_1ARGLEUF81 - 200
d_25ens_1ASPGLUF202 - 219
d_26ens_1MNMNG
d_27ens_1MNMNH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iron-sulfur cluster repair protein YtfE / Regulator of cell morphogenesis and NO signaling / RCMNS


Mass: 24704.361 Da / Num. of mol.: 2 / Mutation: C30A, C31A, E159L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ytfE, b4209, JW4167
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P69506

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Non-polymers , 6 types, 235 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: Tris-HCl pH 8.5, PEG 4000, magnesium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 1.86→53.39 Å / Num. obs: 43000 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.81 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Net I/σ(I): 13
Reflection shellResolution: 1.86→1.88 Å / Num. unique obs: 2139 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FNN

5fnn


Resolution: 1.86→53.39 Å / SU ML: 0.248 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2047 2089 4.86 %
Rwork0.181 40900 -
obs0.1821 42989 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.43 Å2
Refinement stepCycle: LAST / Resolution: 1.86→53.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 18 227 3705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763576
X-RAY DIFFRACTIONf_angle_d0.79024849
X-RAY DIFFRACTIONf_chiral_restr0.0441544
X-RAY DIFFRACTIONf_plane_restr0.0063633
X-RAY DIFFRACTIONf_dihedral_angle_d12.55861388
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.638809817113 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.34061300.33362742X-RAY DIFFRACTION99.69
1.9-1.950.2821530.26852695X-RAY DIFFRACTION99.62
1.95-20.24281470.22942710X-RAY DIFFRACTION99.55
2-2.060.25831320.20272741X-RAY DIFFRACTION99.69
2.06-2.130.25321390.1942670X-RAY DIFFRACTION99.36
2.13-2.20.22731570.1852708X-RAY DIFFRACTION99.24
2.2-2.290.23551440.19272694X-RAY DIFFRACTION99.23
2.29-2.390.20791310.1942718X-RAY DIFFRACTION99.06
2.39-2.520.21291470.18162715X-RAY DIFFRACTION99
2.52-2.680.19191350.1742710X-RAY DIFFRACTION98.85
2.68-2.880.1931410.18152731X-RAY DIFFRACTION99.31
2.88-3.170.24251430.19862714X-RAY DIFFRACTION99.41
3.17-3.630.22711280.1812755X-RAY DIFFRACTION99.21
3.63-4.580.15321260.14252771X-RAY DIFFRACTION98.54
4.58-53.390.16911360.17172826X-RAY DIFFRACTION98.93
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)
14.58244219613-0.464923869422-0.1083186274313.28827819759-0.246450885564.873703354550.1530797432080.106935604388-0.029355930537-0.178031748596-0.112466098321-0.4639272906880.1388437973260.0592654722744-0.05422776096590.192996248820.0242760240750.00771718345090.208441213320.008100987134350.45874788773120.1232136181-11.570208795241.650260938
21.96411274224-0.0731899139110.06829103077952.74894309843-0.9314692176292.260622635290.09454540518260.053019393732-0.0131967418113-0.142015348026-0.145937660881-0.1016700239980.03999830836420.02232090583680.006119017823110.1209521259110.0114118476923-0.01967164450350.200560997541-0.008664429223820.1907338857582.52155075392-1.7459964110343.399728543
36.35906178116-0.6792015552751.673817939262.326717313582.235929567135.734047127170.103175237938-1.028450400940.7711220954270.999520749639-0.0134282279857-0.963135032332-0.5833001705980.386595746124-0.02174753720021.3793957297-0.302249664587-0.2442843637950.783721645408-0.07503382843310.80468248139226.3826451925-2.497190861510.8780325602
42.40588054994-0.149497938319-1.268827572442.15205375421-0.6743469063134.208014951140.178577043971-0.1706618162950.110560640280.683107498311-0.165573010693-0.0483807786573-0.008560412820130.00789902070545-0.05026395529320.802103773928-0.04664018444840.109633915980.30155821224-0.01496789404490.2484770848619.85898684564-12.2200327323.68915273918
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 60 )AA2 - 601 - 59
22chain 'A' and (resid 61 through 220 )AA61 - 22060 - 219
33chain 'B' and (resid 2 through 60 )BF2 - 601 - 59
44chain 'B' and (resid 61 through 220 )BF61 - 22060 - 219

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