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- PDB-5h1n: Crystal structure of SF173 from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 5h1n
TitleCrystal structure of SF173 from Shigella flexneri
ComponentsUPF0253 protein YaeP
KeywordsUNKNOWN FUNCTION / SF173 / hypothetical protein
Function / homologyUncharacterised protein family UPF0253 / Uncharacterised protein family (UPF0253) / UPF0253 protein YaeP
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.47 Å
AuthorsSeo, M.D. / Seok, S.H. / Jung, B.J.
CitationJournal: To Be Published
Title: Crystal structure of SF173 from Shigella flexneri
Authors: Seo, M.D. / Seok, S.H. / Jung, B.J. / Kim, J.H. / Kim, H.N.
History
DepositionOct 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0253 protein YaeP
B: UPF0253 protein YaeP


Theoretical massNumber of molelcules
Total (without water)16,7722
Polymers16,7722
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-43 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.244, 110.244, 110.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-217-

HOH

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Components

#1: Protein UPF0253 protein YaeP


Mass: 8386.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: M90T / Gene: yaeP, SF0180, S0182.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8K7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium citrate tribasic, CHES/sodium hydroxide pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→34.862 Å / Num. obs: 35663 / % possible obs: 94.1 % / Redundancy: 5.8 % / Net I/σ(I): 1.34
Reflection shellResolution: 1.47→1.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.47→34.862 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.66
RfactorNum. reflection% reflection
Rfree0.2225 1688 4.73 %
Rwork0.2055 --
obs0.2063 35663 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→34.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 0 216 1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151094
X-RAY DIFFRACTIONf_angle_d1.5411478
X-RAY DIFFRACTIONf_dihedral_angle_d11.485402
X-RAY DIFFRACTIONf_chiral_restr0.065168
X-RAY DIFFRACTIONf_plane_restr0.009192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4703-1.51360.29561480.272659X-RAY DIFFRACTION90
1.5136-1.56240.29061490.23362897X-RAY DIFFRACTION97
1.5624-1.61830.2381410.22842884X-RAY DIFFRACTION97
1.6183-1.68310.24111350.21292873X-RAY DIFFRACTION97
1.6831-1.75970.23851100.22982944X-RAY DIFFRACTION97
1.7597-1.85240.29261480.23192880X-RAY DIFFRACTION97
1.8524-1.96850.24831390.23572880X-RAY DIFFRACTION96
1.9685-2.12050.25621700.19572896X-RAY DIFFRACTION97
2.1205-2.33380.24371240.20632911X-RAY DIFFRACTION96
2.3338-2.67140.23581550.2082885X-RAY DIFFRACTION96
2.6714-3.36520.191400.20152835X-RAY DIFFRACTION93
3.3652-34.8720.18751290.18342431X-RAY DIFFRACTION78

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