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- PDB-6h1j: TarP native -

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Basic information

Entry
Database: PDB / ID: 6h1j
TitleTarP native
ComponentsProbable ss-1,3-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / Staphylococcus aureus / wall teichoic acid / inverting glycosyltransferase / GT-A fold
Function / homology
Function and homology information


teichoic acid biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cell wall organization / metal ion binding
Similarity search - Function
: / Glycosyl transferase TarS linker domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarP
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å
AuthorsGuo, Y. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTRR34, CRC766 Germany
CitationJournal: Nature / Year: 2018
Title: Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity.
Authors: Gerlach, D. / Guo, Y. / De Castro, C. / Kim, S.H. / Schlatterer, K. / Xu, F.F. / Pereira, C. / Seeberger, P.H. / Ali, S. / Codee, J. / Sirisarn, W. / Schulte, B. / Wolz, C. / Larsen, J. / ...Authors: Gerlach, D. / Guo, Y. / De Castro, C. / Kim, S.H. / Schlatterer, K. / Xu, F.F. / Pereira, C. / Seeberger, P.H. / Ali, S. / Codee, J. / Sirisarn, W. / Schulte, B. / Wolz, C. / Larsen, J. / Molinaro, A. / Lee, B.L. / Xia, G. / Stehle, T. / Peschel, A.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ss-1,3-N-acetylglucosaminyltransferase
B: Probable ss-1,3-N-acetylglucosaminyltransferase
C: Probable ss-1,3-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,06915
Polymers119,6663
Non-polymers40312
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.370, 95.250, 125.470
Angle α, β, γ (deg.)90.00, 96.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A18 - 61
2114B18 - 61
3114C18 - 61
1214A85 - 138
2214B85 - 138
3214C85 - 138
1314A151 - 190
2314B151 - 190
3314C151 - 190
1414A197 - 221
2414B197 - 221
3414C197 - 221
1514A244 - 345
2514B244 - 345
3514C244 - 345

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.3808, 0.738816, 0.556006), (-0.353568, -0.43927, 0.825852), (0.854389, -0.51107, 0.093947)-67.89397, 99.83048, 53.91513
3given(0.249476, -0.374479, 0.893044), (0.741189, -0.519659, -0.424963), (0.623218, 0.767933, 0.147917)15.87473, 124.85537, -47.92157

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Components

#1: Protein Probable ss-1,3-N-acetylglucosaminyltransferase


Mass: 39888.680 Da / Num. of mol.: 3 / Mutation: no
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: SA1808 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNB0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 25% PEG 3350, 250 mM magnesium chloride, 0.1 M sodium citrate, pH 5.7.
PH range: 5.4-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.86→44.5 Å / Num. obs: 83739 / % possible obs: 98.5 % / Redundancy: 2.9 % / Net I/σ(I): 9.4
Reflection shellResolution: 1.86→1.91 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.86→44.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.966 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21607 4187 5 %RANDOM
Rwork0.17045 ---
obs0.17277 79552 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.746 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å21.23 Å2
2---1.42 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.86→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7498 0 12 677 8187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0147630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176994
X-RAY DIFFRACTIONr_angle_refined_deg1.311.65210268
X-RAY DIFFRACTIONr_angle_other_deg0.9381.64316323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14523.974380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.528151437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6791528
X-RAY DIFFRACTIONr_chiral_restr0.0720.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021432
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2333.9713746
X-RAY DIFFRACTIONr_mcbond_other2.2293.973745
X-RAY DIFFRACTIONr_mcangle_it3.1535.9124669
X-RAY DIFFRACTIONr_mcangle_other3.1535.9134670
X-RAY DIFFRACTIONr_scbond_it3.1234.5573884
X-RAY DIFFRACTIONr_scbond_other3.1224.5573885
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7186.5685599
X-RAY DIFFRACTIONr_long_range_B_refined7.03938.9632940
X-RAY DIFFRACTIONr_long_range_B_other6.93438.4832537
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3527 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.530.5
Bmedium positional0.530.5
Cmedium positional0.750.5
Amedium thermal2.342
Bmedium thermal3.142
Cmedium thermal3.192
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 304 -
Rwork0.347 5782 -
obs--97.44 %
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)
10.6843-0.9280.1831.6939-0.43250.23780.10870.09840.0139-0.219-0.0852-0.05950.03190.0528-0.02350.23770.01250.09480.0406-0.01520.049722.23448.226233.1266
21.27470.9296-0.68191.3605-0.67250.41890.03630.00950.19290.03430.06760.1013-0.0577-0.0235-0.10390.15510.01340.05850.00640.00190.05134.9576100.09275.7091
30.5223-0.4202-0.73110.62690.54241.7535-0.0139-0.0095-0.06560.0479-0.05320.02310.0231-0.12030.06710.18770.01260.07480.0440.02250.0451-4.484899.762150.4515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 327
2X-RAY DIFFRACTION2B19 - 327
3X-RAY DIFFRACTION3C19 - 327

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