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- PDB-8p20: TarM(Se)_G117R-UDP-4RboP-glucose -

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Basic information

Entry
Database: PDB / ID: 8p20
TitleTarM(Se)_G117R-UDP-4RboP-glucose
ComponentsTarM(Se)_G117R
KeywordsTRANSFERASE / Staphylococcus epidermidis / wall teichoic acid glycosyltransferase / GT-B fold / alpha-O-glucose.
Function / homologyChem-BJT / BETA-MERCAPTOETHANOL / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.848 Å
AuthorsGuo, Y. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC-TR261 Germany
CitationJournal: Sci Adv / Year: 2023
Title: Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition.
Authors: Guo, Y. / Du, X. / Krusche, J. / Beck, C. / Ali, S. / Walter, A. / Winstel, V. / Mayer, C. / Codee, J.D.C. / Peschel, A. / Stehle, T.
History
DepositionMay 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: TarM(Se)_G117R
BBB: TarM(Se)_G117R
CCC: TarM(Se)_G117R
DDD: TarM(Se)_G117R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,67930
Polymers238,6104
Non-polymers7,06926
Water13,223734
1
AAA: TarM(Se)_G117R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3637
Polymers59,6521
Non-polymers1,7116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TarM(Se)_G117R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4347
Polymers59,6521
Non-polymers1,7816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: TarM(Se)_G117R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5199
Polymers59,6521
Non-polymers1,8678
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: TarM(Se)_G117R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3637
Polymers59,6521
Non-polymers1,7116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.620, 75.750, 129.400
Angle α, β, γ (deg.)90.015, 90.039, 90.031
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
TarM(Se)_G117R


Mass: 59652.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 760 molecules

#2: Chemical
ChemComp-BJT / [(2~{R},3~{S},4~{S})-2-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentoxy]phosphoryl]oxy-pentoxy]phosphoryl]oxy-pentyl] [(2~{S},3~{R},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] hydrogen phosphate


Mass: 1036.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H56O34P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 10% PEG 20 000, 25% PEG MME 550, 0.1 M MES/imidazole, pH 6.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium tartrate (racemic), 0.02 M sodium oxamate.
PH range: 6.2-8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99986715688787 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986715688787 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.414
pseudo-merohedral22-H, K, -L20.151
pseudo-merohedral33-h,-k,l30.1626
pseudo-merohedral44h,-k,-l40.2725
ReflectionResolution: 2.848→49.23 Å / Num. obs: 51972 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC1/2: 0.99 / Net I/σ(I): 5.8
Reflection shellResolution: 2.848→2.92 Å / Num. unique obs: 3918 / CC1/2: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.848→49.204 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.004 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2664 2691 5.178 %
Rwork0.2283 49280 -
all0.23 --
obs-51971 99.752 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.793 Å2
Baniso -1Baniso -2Baniso -3
1--13.915 Å215.052 Å2-5.92 Å2
2--55.116 Å231.486 Å2
3----41.201 Å2
Refinement stepCycle: LAST / Resolution: 2.848→49.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14004 0 423 734 15161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01314675
X-RAY DIFFRACTIONr_bond_other_d0.0020.01811482
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.67619988
X-RAY DIFFRACTIONr_angle_other_deg1.4141.60926380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.80351963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62224.202614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.562151880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0211540
X-RAY DIFFRACTIONr_chiral_restr0.0440.22198
X-RAY DIFFRACTIONr_chiral_restr_other0.0210.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216956
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023054
X-RAY DIFFRACTIONr_nbd_refined0.1910.22095
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.210528
X-RAY DIFFRACTIONr_nbtor_refined0.1710.27000
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.26856
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0680.2179
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2970.239
X-RAY DIFFRACTIONr_nbd_other0.2290.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0190.24
X-RAY DIFFRACTIONr_mcbond_it1.97320.027864
X-RAY DIFFRACTIONr_mcbond_other1.97220.0197863
X-RAY DIFFRACTIONr_mcangle_it3.07427.0449823
X-RAY DIFFRACTIONr_mcangle_other3.07427.0459824
X-RAY DIFFRACTIONr_scbond_it1.6619.6796811
X-RAY DIFFRACTIONr_scbond_other1.6619.686810
X-RAY DIFFRACTIONr_scangle_it2.50426.58310165
X-RAY DIFFRACTIONr_scangle_other2.50426.58310166
X-RAY DIFFRACTIONr_lrange_it5.399115.37458632
X-RAY DIFFRACTIONr_lrange_other5.399115.37258633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.848-2.9220.3881990.2973604X-RAY DIFFRACTION97.8893
2.922-3.0020.3541900.2793510X-RAY DIFFRACTION99.2489
3.002-3.0880.3221710.2453548X-RAY DIFFRACTION100.5135
3.088-3.1830.3061740.2483293X-RAY DIFFRACTION100.0866
3.183-3.2870.2631920.2223259X-RAY DIFFRACTION99.5672
3.287-3.4020.2141560.2223169X-RAY DIFFRACTION99.8199
3.402-3.5290.2611660.2342952X-RAY DIFFRACTION99.9359
3.529-3.6730.2771820.2163004X-RAY DIFFRACTION100.2202
3.673-3.8350.2471440.222766X-RAY DIFFRACTION99.5893
3.835-4.0210.3071260.2132649X-RAY DIFFRACTION99.892
4.021-4.2370.2341310.2042573X-RAY DIFFRACTION99.8523
4.237-4.4920.2481700.22390X-RAY DIFFRACTION100.3922
4.492-4.7990.1911320.1932244X-RAY DIFFRACTION99.4558
4.799-5.180.2551030.2112119X-RAY DIFFRACTION100.1803
5.18-5.6680.2731320.2371918X-RAY DIFFRACTION99.8053
5.668-6.3260.2431220.251736X-RAY DIFFRACTION100.0538
6.326-7.2850.237500.2591611X-RAY DIFFRACTION100.1809
7.285-8.8740.271610.211302X-RAY DIFFRACTION99.7074
8.874-12.350.294540.2071044X-RAY DIFFRACTION100.274
12.35-49.2040.3360.339589X-RAY DIFFRACTION99.0491

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