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- PDB-6a07: Salmonella Typhi YfdX in the F222 space group at 1.5 A resolution -

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Basic information

Entry
Database: PDB / ID: 6a07
TitleSalmonella Typhi YfdX in the F222 space group at 1.5 A resolution
ComponentsYfdX protein
KeywordsUNKNOWN FUNCTION / STY3178 / YfdX / Salmonella
Function / homology
Function and homology information


YfdX protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2140 / Uncharacterised protein family YfdX / YfdX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Four Helix Bundle (Hemerythrin (Met), subunit A) / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
YfdX family protein / YfdX family protein
Similarity search - Component
Biological speciesSalmonella enterica I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsKu, B. / Lee, H.S. / Kim, S.J.
CitationJournal: Front Microbiol / Year: 2018
Title: Structural and Physiological Exploration ofSalmonellaTyphi YfdX Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence.
Authors: Lee, H.S. / Lee, S. / Kim, J.S. / Lee, H.R. / Shin, H.C. / Lee, M.S. / Jin, K.S. / Kim, C.H. / Ku, B. / Ryu, C.M. / Kim, S.J.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7956
Polymers20,6301
Non-polymers1655
Water3,927218
1
A: YfdX protein
hetero molecules

A: YfdX protein
hetero molecules

A: YfdX protein
hetero molecules

A: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18024
Polymers82,5204
Non-polymers65920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
crystal symmetry operation11_554-x+1/2,y,-z-1/21
crystal symmetry operation14_545-x+1/2,-y-1/2,z1
Buried area14810 Å2
ΔGint-272 kcal/mol
Surface area26980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.798, 92.207, 95.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein YfdX protein / YfdX from Salmonella Typhi


Mass: 20630.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica I (bacteria) / Gene: yfdX, CVR97_27555, SE14_03224 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7DJF1, UniProt: A0A0D6IF67*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate (pH 4.6), 2.5 M sodium chloride, 12% PEG1500, 1.5% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 31146 / % possible obs: 99.4 % / Redundancy: 6 % / Rpim(I) all: 0.035 / Net I/σ(I): 38.3
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1542 / Rpim(I) all: 0.131

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A02

6a02


Resolution: 1.501→26.56 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 19.37
RfactorNum. reflection% reflection
Rfree0.2152 2021 6.49 %
Rwork0.182 --
obs0.1841 31146 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.501→26.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 5 218 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051351
X-RAY DIFFRACTIONf_angle_d0.721817
X-RAY DIFFRACTIONf_dihedral_angle_d13.121853
X-RAY DIFFRACTIONf_chiral_restr0.046204
X-RAY DIFFRACTIONf_plane_restr0.004239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5011-1.53860.23531360.22152046X-RAY DIFFRACTION99
1.5386-1.58020.24421350.20842059X-RAY DIFFRACTION99
1.5802-1.62670.25441520.20792060X-RAY DIFFRACTION99
1.6267-1.67920.20961320.19672062X-RAY DIFFRACTION99
1.6792-1.73920.24391350.19232071X-RAY DIFFRACTION99
1.7392-1.80890.23071500.19872054X-RAY DIFFRACTION100
1.8089-1.89120.22981350.19022082X-RAY DIFFRACTION100
1.8912-1.99080.22031470.19312060X-RAY DIFFRACTION100
1.9908-2.11550.1941560.17972080X-RAY DIFFRACTION100
2.1155-2.27880.21541530.17512082X-RAY DIFFRACTION100
2.2788-2.50790.22931500.19142088X-RAY DIFFRACTION100
2.5079-2.87050.22971390.18822103X-RAY DIFFRACTION100
2.8705-3.61510.19641520.16812114X-RAY DIFFRACTION100
3.6151-26.56390.20151490.16622164X-RAY DIFFRACTION98

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