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- PDB-6ejj: Structure of a glycosyltransferase / state 2 -

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Basic information

Entry
Database: PDB / ID: 6ejj
TitleStructure of a glycosyltransferase / state 2
ComponentsWlaC protein
KeywordsTRANSFERASE / Glycosyltransferase
Function / homology
Function and homology information


UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid biosynthetic process / nucleotide binding
Similarity search - Function
Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
NerylNeryl pyrophosphate / URIDINE-5'-DIPHOSPHATE / WlaC protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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.id / _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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_type.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)89,22813
Polymers86,1362
Non-polymers3,09211
Water81145
1
A: WlaC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6327
Polymers43,0681
Non-polymers1,5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WlaC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5966
Polymers43,0681
Non-polymers1,5285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.510, 125.780, 71.010
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein WlaC protein / Glycosyltransferase


Mass: 43067.895 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

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Non-polymers , 5 types, 54 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BUE / NerylNeryl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H36O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
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: Nov 18, 2016
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48793 / % possible obs: 96.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.212 / Net I/σ(I): 5.6
Reflection shellResolution: 2.7→2.796 Å / Rmerge(I) obs: 1.743 / Mean I/σ(I) obs: 1.69 / % possible all: 100

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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: 2.7→29.814 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.2444 1479 5.15 %
Rwork0.2062 --
obs0.2082 28715 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 0 161 45 6034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056098
X-RAY DIFFRACTIONf_angle_d0.868226
X-RAY DIFFRACTIONf_dihedral_angle_d18.2153638
X-RAY DIFFRACTIONf_chiral_restr0.053944
X-RAY DIFFRACTIONf_plane_restr0.0041010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78710.38041270.31672390X-RAY DIFFRACTION96
2.7871-2.88660.33871360.29912510X-RAY DIFFRACTION99
2.8866-3.00210.30451370.30282493X-RAY DIFFRACTION99
3.0021-3.13860.31891350.28812449X-RAY DIFFRACTION98
3.1386-3.30390.35441500.27412450X-RAY DIFFRACTION98
3.3039-3.51060.3011220.23882483X-RAY DIFFRACTION98
3.5106-3.78110.24721360.18072427X-RAY DIFFRACTION97
3.7811-4.16070.19771250.17012510X-RAY DIFFRACTION100
4.1607-4.76070.20031340.1552512X-RAY DIFFRACTION99
4.7607-5.990.2161550.182502X-RAY DIFFRACTION99
5.99-29.81620.18571220.1842510X-RAY DIFFRACTION98

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