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- PDB-6h21: TarP-UDP-GlcNAc-Mn -

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Basic information

Entry
Database: PDB / ID: 6h21
TitleTarP-UDP-GlcNAc-Mn
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
: / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarP
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 12, 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 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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)122,43626
Polymers119,6663
Non-polymers2,77023
Water12,701705
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)43.860, 95.360, 130.550
Angle α, β, γ (deg.)90.00, 93.51, 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(0.388818, 0.75149, 0.532994), (-0.333424, -0.424526, 0.841788), (0.858865, -0.505016, 0.085502)-54.53655, 104.30943, 34.59565
3given(0.304268, -0.409083, 0.860275), (0.682977, -0.535865, -0.496377), (0.664051, 0.73858, 0.116347)33.98381, 113.35099, -59.33849

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 39888.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: SA1808 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNB0

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Non-polymers , 6 types, 728 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 705 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
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: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→47.7 Å / Num. obs: 99074 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rsym value: 0.056 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H1J

6h1j


Resolution: 1.8→47.68 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.275 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21149 4954 5 %RANDOM
Rwork0.17563 ---
obs0.17744 94120 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.575 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å2-0 Å21.23 Å2
2---2.14 Å20 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7483 0 147 705 8335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0147747
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176990
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.67710453
X-RAY DIFFRACTIONr_angle_other_deg0.9241.65816320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56324.063379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.191151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4721527
X-RAY DIFFRACTIONr_chiral_restr0.0630.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028489
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021450
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_it1.2721.6573754
X-RAY DIFFRACTIONr_mcbond_other1.271.6573753
X-RAY DIFFRACTIONr_mcangle_it1.982.4614679
X-RAY DIFFRACTIONr_mcangle_other1.982.4614680
X-RAY DIFFRACTIONr_scbond_it1.5711.9673993
X-RAY DIFFRACTIONr_scbond_other1.5711.9673993
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.222.8795774
X-RAY DIFFRACTIONr_long_range_B_refined7.58716.28333454
X-RAY DIFFRACTIONr_long_range_B_other7.58716.28233454
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: 3498 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.430.5
Bmedium positional0.40.5
Cmedium positional0.420.5
Amedium thermal2.212
Bmedium thermal2.072
Cmedium thermal1.492
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 363 -
Rwork0.326 6898 -
obs--99.44 %
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)
10.6891-0.49410.3281.2342-0.53130.32930.15930.0741-0.0975-0.138-0.0837-0.02410.28190.1009-0.07570.64690.1217-0.04360.3218-0.01410.370446.09848.108334.2529
20.90030.8112-0.50352.0861-0.71890.3632-0.01290.01260.09580.0890.05810.0311-0.0325-0.0386-0.04520.02430.0216-0.04150.2424-0.00650.351157.4723100.12176.0751
30.445-0.3163-1.06650.54130.93752.73510.0737-0.013-0.01720.1848-0.0891-0.0172-0.1413-0.14970.01540.31840.06760.00760.35740.01580.388321.273699.029153.728
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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