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- PDB-6ejk: Structure of a glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 6ejk
TitleStructure of a glycosyltransferase
ComponentsWlaC protein
KeywordsTRANSFERASE / Glycosyltransferase
Function / homologyGlycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / NerylNeryl pyrophosphate / Chem-UDN / WlaC protein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRamirez, A.S. / Boilevin, J. / Mehdipour, A.R. / Hummer, G. / Darbre, T. / Reymond, J.L. / Locher, K.P.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.
Authors: Ramirez, A.S. / Boilevin, J. / Mehdipour, A.R. / Hummer, G. / Darbre, T. / Reymond, J.L. / Locher, K.P.
History
DepositionSep 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WlaC protein
B: WlaC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8788
Polymers86,5112
Non-polymers3,3676
Water0
1
A: WlaC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9394
Polymers43,2551
Non-polymers1,6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WlaC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9394
Polymers43,2551
Non-polymers1,6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.870, 126.910, 71.090
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein WlaC protein / glycosyltransferase


Mass: 43255.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O86151
#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAca1-4DGalpNAca1-3DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O]/1-2-2/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-D-GalpNAc]{[(4+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-UDN / Uridine-Diphosphate-Methylene-N-acetyl-galactosamine


Mass: 605.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H29N3O16P2
#4: Chemical ChemComp-BUE / NerylNeryl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H36O7P2

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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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Ammonium acetate, ADA, PEG3350

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 23160 / % possible obs: 95.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.1772 / Net I/σ(I): 6.1
Reflection shellResolution: 3.3→3.418 Å / Rmerge(I) obs: 0.9563 / Mean I/σ(I) obs: 1.91 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EJI

6eji


Resolution: 3.3→29.89 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.254 832 5.17 %
Rwork0.211 --
obs0.213 16100 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 0 184 0 6012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126128
X-RAY DIFFRACTIONf_angle_d1.3578270
X-RAY DIFFRACTIONf_dihedral_angle_d17.5013654
X-RAY DIFFRACTIONf_chiral_restr0.064946
X-RAY DIFFRACTIONf_plane_restr0.0081012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.50650.33071390.28012553X-RAY DIFFRACTION99
3.5065-3.77670.28981420.25472475X-RAY DIFFRACTION96
3.7767-4.15590.28751510.21162529X-RAY DIFFRACTION100
4.1559-4.75520.22791270.18292580X-RAY DIFFRACTION100
4.7552-5.98320.24321430.20912550X-RAY DIFFRACTION99
5.9832-29.89240.21741300.19072581X-RAY DIFFRACTION98
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)
14.1961-2.34812.3975.8102-1.54737.0880.0556-0.0392-0.1183-0.48080.0575-0.07870.7219-0.0928-0.06850.42210.04050.09390.4855-0.14790.302683.8671-16.6620.7302
26.2027-1.13622.99492.5612-0.28935.2973-0.2512-0.26590.3590.2950.0623-0.2259-0.40480.24510.09450.3983-0.00120.00040.3550.01580.416378.1088-4.044227.0457
36.7934-1.46991.95912.4527-0.16463.5519-0.1201-0.0988-0.26130.09980.06250.3376-0.0475-0.27350.08770.41110.01150.05360.34120.06250.40859.5768-1.775115.2003
44.07982.6705-2.96067.4594-2.93176.80840.37640.0241-0.32440.5574-0.1202-0.4084-0.75170.1322-0.35810.4706-0.0398-0.05390.5028-0.14050.35490.8572-37.893615.3942
57.1890.3648-4.04543.7249-0.46075.27150.04520.3748-0.336-0.3189-0.1369-0.1010.2939-0.11390.16310.3262-0.0005-0.08730.3987-0.01440.489385.1276-50.3398.5835
66.79131.7375-3.12661.7349-0.98444.0495-0.0410.33060.3338-0.09660.05510.2905-0.0216-0.23490.03850.4346-0.0349-0.09810.3687-0.02320.49166.5478-53.107220.3732
72.98890.5904-1.24274.01393.09424.22920.3110.51940.63990.68422.0840.29721.3708-0.2896-2.73021.9509-0.02860.11771.41850.05551.382472.1078-16.758426.1359
85.4802-2.209-0.32224.74784.96836.0876-0.0369-0.9901-0.2827-0.59180.798-0.2883-1.16750.5525-0.18911.7025-0.21180.14621.57480.61981.627779.0536-37.91429.9938
95.90890.4781-3.48582.3329-2.19093.81661.3676-1.3993-0.2805-0.32220.39270.46970.33560.1522-0.75340.78280.2727-0.01921.17060.0791.267567.6597-7.405318.3432
102.720.1622-0.59642.5796-2.1282.76810.96020.62290.49820.3876-0.4176-0.08130.19040.3689-0.46830.9232-0.3931-0.25171.86540.15380.83374.7289-47.324317.3478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 84 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 85 THROUGH 184 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 185 THROUGH 360 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 84 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 85 THROUGH 184 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 185 THROUGH 360 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 402 THROUGH 405 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 402 THROUGH 405 )
9X-RAY DIFFRACTION9CHAIN 'A' AND RESSEQ 401
10X-RAY DIFFRACTION10CHAIN 'B' AND RESSEQ 401

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