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- PDB-4wli: Stationary Phase Survival Protein YuiC from B.subtilis -

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Basic information

Entry
Database: PDB / ID: 4wli
TitleStationary Phase Survival Protein YuiC from B.subtilis
ComponentsYuiC
KeywordsLYASE / lytic transglycosylase / peptidoglycan remodelling / stationary phase / MltA
Function / homology3D domain / 3D domain / RlpA-like domain superfamily / peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / Uncharacterized protein YuiC
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsQuay, D.H.X. / Cole, A.R. / Cryar, A. / Thalassinos, K. / Williams, M.A. / Bhakta, S. / Keep, N.H.
CitationJournal: Bmc Struct.Biol. / Year: 2015
Title: Structure of the stationary phase survival protein YuiC from B.subtilis.
Authors: Quay, D.H. / Cole, A.R. / Cryar, A. / Thalassinos, K. / Williams, M.A. / Bhakta, S. / Keep, N.H.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: YuiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4935
Polymers16,2451
Non-polymers2484
Water2,306128
1
A: YuiC
hetero molecules

A: YuiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,98710
Polymers32,4902
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9470 Å2
ΔGint-37 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.010, 117.270, 61.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-476-

HOH

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Components

#1: Protein YuiC


Mass: 16245.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yuiC, BSU32070 / Plasmid: pNic28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta-2 / References: UniProt: O32108
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium chloride, 25 (v/v) glycerol ethoxylate, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.76→30.8 Å / Num. obs: 18150 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJT

4wjt


Resolution: 1.76→30.798 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 927 5.11 %
Rwork0.1622 --
obs0.1642 18131 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→30.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 16 128 1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161161
X-RAY DIFFRACTIONf_angle_d1.4951574
X-RAY DIFFRACTIONf_dihedral_angle_d12.586434
X-RAY DIFFRACTIONf_chiral_restr0.068172
X-RAY DIFFRACTIONf_plane_restr0.009202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7601-1.85290.24751260.20082403X-RAY DIFFRACTION100
1.8529-1.96890.23511340.18942414X-RAY DIFFRACTION100
1.9689-2.12090.22021200.16232442X-RAY DIFFRACTION100
2.1209-2.33430.17411390.1492424X-RAY DIFFRACTION99
2.3343-2.67190.21441260.15572469X-RAY DIFFRACTION100
2.6719-3.36560.18991520.16862469X-RAY DIFFRACTION100
3.3656-30.80270.19731300.15462583X-RAY DIFFRACTION99
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)
12.904-0.047-0.13560.7235-0.71221.32380.05860.11070.4690.1215-0.05160.0239-0.08770.06010.03170.1611-0.0070.01580.17580.01930.19688.646226.27662.6285
20.59290.26420.58392.75140.99020.81410.0722-0.1174-0.12350.1995-0.04050.01770.33820.0683-0.0750.2494-0.00310.02170.15140.00320.15269.52496.29485.6423
31.09-0.5620.06031.2013-0.35611.04380.0190.0899-0.0044-0.18040.00790.10540.0784-0.09150.00890.1348-0.0109-0.00010.1380.00820.12657.036719.3228-1.2621
41.1047-0.0846-1.7882.22060.65053.01270.0722-0.20640.08740.0225-0.019-0.03760.0910.1887-0.04830.1501-0.01230.00120.21340.00470.15023.911818.728512.4314
50.54941.0319-0.20781.9407-0.31792.7156-0.1432-0.06820.3006-0.03030.1978-0.1496-0.00130.2605-0.05220.1419-0.01980.01230.1512-0.04350.1747-4.849428.751228.7186
61.30240.3017-0.19862.5421.22131.9063-0.0944-0.4111-0.08780.41740.18270.39660.2472-0.0010.00340.250.00320.06390.23350.02170.1757-15.211314.916238.5794
71.4835-1.31410.61826.7847-2.56750.984-0.0096-0.1153-0.21910.0644-0.02390.7690.231-0.26880.04490.1582-0.02490.05050.1876-0.02510.2547-21.281211.666929.0655
82.7923-0.7686-0.51083.4940.41853.904-0.02720.64480.1155-0.484-0.25170.0879-0.0998-0.04510.19720.23770.0163-0.05680.3182-0.02060.2429-22.290921.126620.043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 73 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 193 )
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 201 )
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 214 )

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