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- PDB-7bhc: Escherichia coli YtfE E125L -

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Basic information

Entry
Database: PDB / ID: 7bhc
TitleEscherichia coli YtfE E125L
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: 1.87 Å
AuthorsSilva, L.S.O. / Matias, P.M. / 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: Front Microbiol / Year: 2021
Title: Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis.
Authors: Silva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, L.M.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_name_com / entity_src_gen / pdbx_initial_refinement_model / pdbx_refine_tls_group / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)50,03212
Polymers49,4092
Non-polymers62410
Water5,819323
1
A: Iron-sulfur cluster repair protein YtfE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1087
Polymers24,7041
Non-polymers4046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron-sulfur cluster repair protein YtfE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9245
Polymers24,7041
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.790, 49.608, 87.819
Angle α, β, γ (deg.)90.000, 100.143, 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-ID
d_1ens_1
d_2ens_1

NCS oper: (Code: givenMatrix: (0.944226147871, -0.0172804015172, 0.328843989454), (-0.0145666260032, -0.999836493473, -0.0107144634333), (0.328975371545, 0.00532672912634, -0.944323477879)Vector: 15. ...NCS oper: (Code: given
Matrix: (0.944226147871, -0.0172804015172, 0.328843989454), (-0.0145666260032, -0.999836493473, -0.0107144634333), (0.328975371545, 0.00532672912634, -0.944323477879)
Vector: 15.6870589063, -21.9455057507, -90.3458090023)

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Components

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


Mass: 24704.359 Da / Num. of mol.: 2 / Mutation: C30A C31A E125L
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
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 59.43 % / Description: needle shaped
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris-HCl, PEG 4000, Magnesium chloride, Sodium Chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→53.2 Å / Num. obs: 41865 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.049 / Rrim(I) all: 0.096 / Net I/σ(I): 9.7
Reflection shellResolution: 1.87→1.98 Å / Rmerge(I) obs: 1.232 / Num. unique obs: 4140 / CC1/2: 0.36 / Rpim(I) all: 0.767 / % possible all: 99.74

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FNN

5fnn


Resolution: 1.87→53.2 Å / SU ML: 0.2826 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7718 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2106 2037 4.87 %
Rwork0.1824 39805 -
obs0.1838 41842 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.76 Å2
Refinement stepCycle: LAST / Resolution: 1.87→53.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 30 323 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253621
X-RAY DIFFRACTIONf_angle_d0.52874909
X-RAY DIFFRACTIONf_chiral_restr0.035548
X-RAY DIFFRACTIONf_plane_restr0.0033642
X-RAY DIFFRACTIONf_dihedral_angle_d14.99622267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.38161330.35782633X-RAY DIFFRACTION99.68
1.92-1.970.3161540.31992578X-RAY DIFFRACTION99.89
1.97-2.020.30451360.2892657X-RAY DIFFRACTION99.86
2.02-2.080.29821310.25662638X-RAY DIFFRACTION99.75
2.08-2.150.29251370.2382657X-RAY DIFFRACTION99.57
2.15-2.220.27241480.21412606X-RAY DIFFRACTION99.67
2.22-2.310.20981460.19512611X-RAY DIFFRACTION99.71
2.31-2.420.20271210.18412647X-RAY DIFFRACTION99.78
2.42-2.540.21410.17632650X-RAY DIFFRACTION99.82
2.54-2.70.2221370.18072666X-RAY DIFFRACTION100
2.7-2.910.22521350.17722647X-RAY DIFFRACTION99.78
2.91-3.20.23391370.18452667X-RAY DIFFRACTION99.93
3.2-3.670.22151260.16162682X-RAY DIFFRACTION99.89
3.67-4.620.15151220.13292714X-RAY DIFFRACTION99.82
4.62-53.20.15611330.17342752X-RAY DIFFRACTION99.45
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)
15.07756933663-0.361676695461-0.1465230413473.898894177450.6497824312318.829107032510.07452647953080.217920291160.0175221125329-0.244533017932-0.0685505164938-0.2843647077050.101552023015-0.04442892505660.01904322753730.1896832448140.01540927317240.02627924677990.1691892700260.02422113352240.367482727587-83.9955856599-14.5756250531-45.0968850749
21.89943623496-0.04726401510860.08143932158262.52255632992-0.6558758595352.765195544530.08122346777360.06867868116770.0289264824497-0.127294611188-0.112151525684-0.0834916409079-0.0608589186582-0.02709943143330.003459867388010.1518616675130.02078778266390.01676745752570.217467402915-0.01376022770720.199931986441-101.417768589-4.65505150815-43.6418839808
33.171578316090.9293119919332.892367782945.297392794541.86247653433.353022659340.285530786293-0.9335642147360.2111992835371.29244543503-0.121493392732-1.08006220618-0.6354336134190.352892564316-0.0786378210651.0991808343-0.237449777821-0.1810942628060.802939873143-0.02491069594230.741246468055-77.8316485678-5.28531377906-75.6036767199
42.85369574880.0928686721035-1.321787484513.20448543703-1.845696336345.871695482270.117342335693-0.223734557325-0.003046129806460.341780637253-0.180832296045-0.1320093309380.08009805256640.07201034885010.04347740352540.445103181861-0.03925949303040.02767834585370.313270554411-0.03774151855480.229168751553-94.283180276-15.3334531681-82.6727997889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2-60 }A2 - 60
2X-RAY DIFFRACTION2{ A|61-220 }A61 - 220
3X-RAY DIFFRACTION3{ B|2-60 }B2 - 60
4X-RAY DIFFRACTION4{ B|61-220 }B61 - 220

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