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- PDB-7bha: Escherichia coli YtfE -

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Basic information

Entry
Database: PDB / ID: 7bha
TitleEscherichia coli YtfE
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
Repair of iron centres family / Iron-sulfur cluster repair protein YftE / 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: 2.19 Å
AuthorsSilva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, L.M.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaSFRH/BD/118545/2016 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 / 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 / _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

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)49,7889
Polymers49,4412
Non-polymers3477
Water1,49583
1
A: Iron-sulfur cluster repair protein YtfE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9405
Polymers24,7201
Non-polymers2204
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)24,8484
Polymers24,7201
Non-polymers1283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.061, 50.647, 87.847
Angle α, β, γ (deg.)90.000, 100.538, 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: (0.937154934584, -0.0127426509258, 0.348680732808), (-0.0132090181169, -0.999912216244, -0.00104002253238), (0.348663376948, -0.00363106786838, -0.937240985511)Vector: - ...NCS oper: (Code: given
Matrix: (0.937154934584, -0.0127426509258, 0.348680732808), (-0.0132090181169, -0.999912216244, -0.00104002253238), (0.348663376948, -0.00363106786838, -0.937240985511)
Vector: -7.56983933579, -20.488964346, 43.352369672)

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Components

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


Mass: 24720.316 Da / Num. of mol.: 2 / Mutation: C30A C31A
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.19 Å3/Da / Density % sol: 54.5 % / Description: needle shapped
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris-HCl, PEG 4000, magnesium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.7314 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7314 Å / Relative weight: 1
ReflectionResolution: 2.188→59.05 Å / Num. obs: 23568 / % possible obs: 87 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.78 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Net I/σ(I): 9.8
Reflection shellResolution: 2.188→2.188 Å / Rmerge(I) obs: 1.548 / Num. unique obs: 549 / CC1/2: 0.354 / % possible all: 40.2

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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: 2.19→59.05 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Structure refined with anomalous data
RfactorNum. reflection% reflection
Rfree0.2496 2235 4.92 %
Rwork0.2117 43180 -
obs0.2136 23498 86.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.67 Å2
Refinement stepCycle: LAST / Resolution: 2.19→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 12 83 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183490
X-RAY DIFFRACTIONf_angle_d0.46444724
X-RAY DIFFRACTIONf_chiral_restr0.0334529
X-RAY DIFFRACTIONf_plane_restr0.003618
X-RAY DIFFRACTIONf_dihedral_angle_d12.40871347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.349730.33181256X-RAY DIFFRACTION40.78
2.24-2.290.3977680.31871531X-RAY DIFFRACTION48.68
2.29-2.350.31211000.29111868X-RAY DIFFRACTION60.57
2.35-2.410.28031140.28522404X-RAY DIFFRACTION74.85
2.41-2.480.34941450.26182882X-RAY DIFFRACTION93.48
2.48-2.560.3171570.25522984X-RAY DIFFRACTION95.73
2.56-2.650.31761250.25912991X-RAY DIFFRACTION95.32
2.65-2.760.3491580.26023006X-RAY DIFFRACTION96.64
2.76-2.880.23881560.2593009X-RAY DIFFRACTION96.32
2.88-3.030.31971640.23843037X-RAY DIFFRACTION96.59
3.03-3.220.23961870.24462950X-RAY DIFFRACTION96.91
3.22-3.470.26781280.22663054X-RAY DIFFRACTION96.51
3.47-3.820.20171650.18953071X-RAY DIFFRACTION97.88
3.82-4.380.21391430.1623065X-RAY DIFFRACTION97.6
4.38-5.510.21361920.16553043X-RAY DIFFRACTION99.2
5.51-59.050.23021600.18843029X-RAY DIFFRACTION97.02

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