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- PDB-7qnt: TarM(Se) native -

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Basic information

Entry
Database: PDB / ID: 7qnt
TitleTarM(Se) native
ComponentsTarM(Se)
KeywordsTRANSFERASE / glycosylate alpha-O-glucose wall teichoic acid fold-B
Function / homologyBETA-MERCAPTOETHANOL
Function and homology information
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.21 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 22, 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)
BBB: TarM(Se)
CCC: TarM(Se)
DDD: TarM(Se)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,05123
Polymers230,2654
Non-polymers78619
Water4,756264
1
AAA: TarM(Se)
hetero molecules

AAA: TarM(Se)
hetero molecules

AAA: TarM(Se)
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 173 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)173,25215
Polymers172,6993
Non-polymers55312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area4970 Å2
ΔGint-29 kcal/mol
Surface area68280 Å2
MethodPISA
2
BBB: TarM(Se)
hetero molecules

BBB: TarM(Se)
hetero molecules

BBB: TarM(Se)
hetero molecules


  • defined by author&software
  • 173 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)173,23018
Polymers172,6993
Non-polymers53215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area4340 Å2
ΔGint-34 kcal/mol
Surface area67880 Å2
MethodPISA
3
CCC: TarM(Se)
hetero molecules

CCC: TarM(Se)
hetero molecules

CCC: TarM(Se)
hetero molecules


  • defined by author&software
  • 173 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)173,33215
Polymers172,6993
Non-polymers63312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5490 Å2
ΔGint-60 kcal/mol
Surface area67460 Å2
MethodPISA
4
DDD: TarM(Se)
hetero molecules

DDD: TarM(Se)
hetero molecules

DDD: TarM(Se)
hetero molecules


  • defined by author&software
  • 173 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)173,33721
Polymers172,6993
Non-polymers63818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_435-y-1,x-y-2,z1
crystal symmetry operation3_645-x+y+1,-x-1,z1
Buried area4980 Å2
ΔGint-68 kcal/mol
Surface area69010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.010, 154.010, 207.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
TarM(Se)


Mass: 57566.230 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)
References: poly(ribitol-phosphate) alpha-N-acetylglucosaminyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 15% PEG 1000, 6 mM hexaamminecobalt (III) chloride, 0.1 M tris/HCl
PH range: 6.6-8.1

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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: Feb 7, 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, L10.5633
pseudo-merohedral22-K, -H, -L20.4367
ReflectionResolution: 3.21→48.99 Å / Num. obs: 45535 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 15.57
Reflection shellResolution: 3.21→3.29 Å / Redundancy: 20 % / Num. unique obs: 3341 / CC1/2: 0.51 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS2021-04data reduction
XSCALE2021-02data scaling
PHASER2.1.2phasing
RefinementMethod to determine structure: MIR / Resolution: 3.21→48.99 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.211 / SU B: 18.578 / SU ML: 0.358 / Average fsc free: 0.942 / Average fsc work: 0.9539 / Cross valid method: FREE R-VALUE / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2572 2341 5.141 %
Rwork0.2277 43192 -
all0.229 --
obs-45533 99.982 %
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: 73.288 Å2
Baniso -1Baniso -2Baniso -3
1-0.137 Å20 Å20 Å2
2--0.137 Å20 Å2
3----0.274 Å2
Refinement stepCycle: LAST / Resolution: 3.21→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13389 0 28 264 13681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01213620
X-RAY DIFFRACTIONr_bond_other_d0.0010.01810317
X-RAY DIFFRACTIONr_angle_refined_deg1.021.64118603
X-RAY DIFFRACTIONr_angle_other_deg1.4661.58123443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.10151963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17124.065556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.637151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9191531
X-RAY DIFFRACTIONr_chiral_restr0.0340.22053
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022912
X-RAY DIFFRACTIONr_nbd_refined0.2170.22120
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.28796
X-RAY DIFFRACTIONr_nbtor_refined0.1680.26711
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.26095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0790.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.231
X-RAY DIFFRACTIONr_nbd_other0.2410.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.26
X-RAY DIFFRACTIONr_mcbond_it2.78932.3947864
X-RAY DIFFRACTIONr_mcbond_other2.78732.3947863
X-RAY DIFFRACTIONr_mcangle_it4.52943.7399823
X-RAY DIFFRACTIONr_mcangle_other4.52943.7399824
X-RAY DIFFRACTIONr_scbond_it2.24829.4835756
X-RAY DIFFRACTIONr_scbond_other2.24829.4835757
X-RAY DIFFRACTIONr_scangle_it3.52240.3048780
X-RAY DIFFRACTIONr_scangle_other3.52140.3048781
X-RAY DIFFRACTIONr_lrange_it8.077179.03753583
X-RAY DIFFRACTIONr_lrange_other8.077179.03653584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.2930.3411630.2553162X-RAY DIFFRACTION99.76
3.293-3.3830.3631520.2853090X-RAY DIFFRACTION100
3.383-3.480.3271720.2653000X-RAY DIFFRACTION100
3.48-3.5870.3331760.272919X-RAY DIFFRACTION100
3.587-3.7040.321690.2572814X-RAY DIFFRACTION100
3.704-3.8330.2671350.242747X-RAY DIFFRACTION100
3.833-3.9770.311420.2432676X-RAY DIFFRACTION100
3.977-4.1380.2831420.2242531X-RAY DIFFRACTION100
4.138-4.320.2421330.2172434X-RAY DIFFRACTION100
4.32-4.530.2241260.2172389X-RAY DIFFRACTION100
4.53-4.7720.241220.212208X-RAY DIFFRACTION100
4.772-5.0590.2311270.2172093X-RAY DIFFRACTION100
5.059-5.4040.2461180.2311960X-RAY DIFFRACTION100
5.404-5.8310.23950.2511863X-RAY DIFFRACTION100
5.831-6.3790.268790.2571730X-RAY DIFFRACTION100
6.379-7.1160.327760.261544X-RAY DIFFRACTION100
7.116-8.1890.207790.2221387X-RAY DIFFRACTION100
8.189-9.960.221590.1721166X-RAY DIFFRACTION100
9.96-13.8030.178500.155922X-RAY DIFFRACTION100
13.803-48.990.195260.233557X-RAY DIFFRACTION100

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