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- PDB-7qh9: TarM(Se)_G117R-4RboP -

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Basic information

Entry
Database: PDB / ID: 7qh9
TitleTarM(Se)_G117R-4RboP
ComponentsTarM(Se)_G117R-4RboP
KeywordsTRANSFERASE / Staphylococcus epidermidis / glycosyltransferase / GT-B fold / alpha-O-glucose / wall teichoic acid
Function / homologyChem-CWI
Function and homology information
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.689 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
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: TarM(Se)_G117R-4RboP
BBB: TarM(Se)_G117R-4RboP
CCC: TarM(Se)_G117R-4RboP
DDD: TarM(Se)_G117R-4RboP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,94513
Polymers238,6104
Non-polymers2,3359
Water4,324240
1
AAA: TarM(Se)_G117R-4RboP
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 60.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,1792
Polymers59,6521
Non-polymers5261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TarM(Se)_G117R-4RboP
hetero molecules


  • defined by author
  • 60.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,2413
Polymers59,6521
Non-polymers5882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: TarM(Se)_G117R-4RboP
hetero molecules


  • defined by author
  • 60.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,2504
Polymers59,6521
Non-polymers5973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: TarM(Se)_G117R-4RboP
hetero molecules


  • defined by author
  • 60.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,2764
Polymers59,6521
Non-polymers6243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.870, 70.570, 137.380
Angle α, β, γ (deg.)89.971, 90.013, 90.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TarM(Se)_G117R-4RboP


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)
#2: Chemical
ChemComp-CWI / [(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] [(2~{S},3~{R},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] hydrogen phosphate


Mass: 526.216 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H25O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.58 %
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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.3312
pseudo-merohedral22h,-k,-l20.1976
pseudo-merohedral33-h,-k,l30.2171
pseudo-merohedral44-H, K, -L40.2542
ReflectionResolution: 2.689→49.237 Å / Num. obs: 58472 / % possible obs: 95.2 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 9.98
Reflection shellResolution: 2.689→2.76 Å / Num. unique obs: 4412 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.689→49.235 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.226 / SU B: 9.291 / SU ML: 0.213 / Average fsc free: 0.9543 / Average fsc work: 0.9628 / Cross valid method: FREE R-VALUE / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2528 2863 4.896 %
Rwork0.2426 55608 -
all0.243 --
obs-58471 95.069 %
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: 79.364 Å2
Baniso -1Baniso -2Baniso -3
1-48.702 Å2-9.668 Å210.084 Å2
2--19.675 Å21.775 Å2
3----68.377 Å2
Refinement stepCycle: LAST / Resolution: 2.689→49.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13997 0 135 240 14372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314371
X-RAY DIFFRACTIONr_bond_other_d0.0020.01811302
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.65119576
X-RAY DIFFRACTIONr_angle_other_deg1.4431.58925911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.36851963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28524.475628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.582151875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1661531
X-RAY DIFFRACTIONr_chiral_restr0.0620.22107
X-RAY DIFFRACTIONr_chiral_restr_other1.7330.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023001
X-RAY DIFFRACTIONr_nbd_refined0.1820.22189
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.29810
X-RAY DIFFRACTIONr_nbtor_refined0.1590.26616
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3160.213
X-RAY DIFFRACTIONr_nbd_other0.2730.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5570.22
X-RAY DIFFRACTIONr_mcbond_it7.68432.9367864
X-RAY DIFFRACTIONr_mcbond_other7.68332.9347863
X-RAY DIFFRACTIONr_mcangle_it10.56544.4699823
X-RAY DIFFRACTIONr_mcangle_other10.56544.4719824
X-RAY DIFFRACTIONr_scbond_it7.46631.996507
X-RAY DIFFRACTIONr_scbond_other7.46631.9876508
X-RAY DIFFRACTIONr_scangle_it10.01243.2549753
X-RAY DIFFRACTIONr_scangle_other10.01143.2519754
X-RAY DIFFRACTIONr_lrange_it14.99187.09956638
X-RAY DIFFRACTIONr_lrange_other14.989187.09756639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.689-2.7580.4722120.35240860.35845290.9540.96894.89950.344
2.758-2.8340.3252440.340490.30144220.9780.98497.08280.293
2.834-2.9150.412180.27839910.28442890.9760.98798.13480.266
2.915-3.0050.3151810.29139220.29241860.9810.98398.01720.273
3.005-3.1030.3792130.27337800.27940840.9610.97997.77180.248
3.103-3.2110.3231880.28236070.28438860.9570.96997.65830.261
3.211-3.3320.31900.29535310.29637940.9410.95998.07590.275
3.332-3.4670.2811600.26433980.26536270.9620.96898.09760.239
3.467-3.6210.3951650.28332000.28734870.9440.95596.50130.258
3.621-3.7970.376540.29418220.29633290.9440.94856.35330.27
3.797-4.0010.2281090.26129910.2632000.950.9596.8750.239
4.001-4.2410.2241590.24127790.2430110.9490.95297.57560.224
4.241-4.5320.1981340.22626050.22428320.9590.95496.71610.209
4.532-4.8920.2921330.21324720.21726640.9210.95497.78530.2
4.892-5.3530.1881280.22522000.22324000.9550.946970.21
5.353-5.9760.2711170.23919890.24121610.9260.93597.45490.222
5.976-6.8840.335720.24617950.24919390.8880.93496.28670.233
6.884-8.390.188930.21315190.21216540.9420.93897.46070.217
8.39-11.6960.155590.15911880.15912810.9650.9697.34580.182
11.696-49.2150.186340.2326840.2297290.9580.9498.49110.265

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