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- PDB-6fi2: VexL: A periplasmic depolymerase provides new insight into ABC tr... -

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Basic information

Entry
Database: PDB / ID: 6fi2
TitleVexL: A periplasmic depolymerase provides new insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides
ComponentsVexL
KeywordsLYASE / Carbohydrate biosynthesis / Cell-surface / Pectate Lyase / Vi antigen
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
Similarity search - Function
AmbAllergen / Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
MALONATE ION / pectate lyase
Similarity search - Component
Biological speciesAchromobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsNaismith, J.H. / McMahon, S.A. / Le Bas, A. / Liston, S.D. / Whitfield, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Periplasmic depolymerase provides insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides.
Authors: Liston, S.D. / McMahon, S.A. / Le Bas, A. / Suits, M.D.L. / Naismith, J.H. / Whitfield, C.
History
DepositionJan 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / 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_special_symmetry / software / 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_struct_special_symmetry.label_asym_id / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VexL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2203
Polymers45,3641
Non-polymers8562
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the sample is a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint2 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.680, 94.680, 78.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-819-

HOH

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Components

#1: Protein VexL


Mass: 45364.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans (bacteria) / Gene: vexL / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160EBC2
#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-galactopyranuronic acid-(1-4)-3-O-acetyl-2-acetamido-2-deoxy-alpha-D- ...2-acetamido-2-deoxy-alpha-D-galactopyranuronic acid-(1-4)-3-O-acetyl-2-acetamido-2-deoxy-alpha-D-galactopyranuronic acid-(1-4)-3-O-acetyl-2-acetamido-2-deoxy-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 753.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2112A-1a_1-5_2*NCC/3=O_3*OCC/3=O][a2112A-1a_1-5_2*NCC/3=O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GalpANAc3Ac]{[(4+1)][a-D-GalpANAc3Ac]{[(4+1)][a-D-GalpANAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.05 Å3/Da / Density % sol: 40 % / Description: rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.58 M sodium malonate, 0.1 M BisTris HCl pH 6.5, 0.13 M ammonium citrate, and 2.5 % (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2017 / Details: Toroidal mirror
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.22→60.6 Å / Num. obs: 106029 / % possible obs: 100 % / Redundancy: 12.8 % / Net I/σ(I): 17
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5241 / CC1/2: 0.778 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
autoPROCdata scaling
BALBESphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→60.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.864 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16621 5200 4.9 %RANDOM
Rwork0.13905 ---
obs0.14038 100829 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---1.16 Å20 Å2
3---2.31 Å2
Refinement stepCycle: 1 / Resolution: 1.22→60.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 59 243 3244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193111
X-RAY DIFFRACTIONr_bond_other_d0.0020.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9594219
X-RAY DIFFRACTIONr_angle_other_deg0.9913.0076491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03923.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6415499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2861527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213546
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02663
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_it1.5241.7091518
X-RAY DIFFRACTIONr_mcbond_other1.5191.7071517
X-RAY DIFFRACTIONr_mcangle_it2.0042.5691901
X-RAY DIFFRACTIONr_mcangle_other2.0032.571902
X-RAY DIFFRACTIONr_scbond_it2.1922.0841593
X-RAY DIFFRACTIONr_scbond_other2.1922.0851594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6463.0032319
X-RAY DIFFRACTIONr_long_range_B_refined3.00321.2893390
X-RAY DIFFRACTIONr_long_range_B_other3.00121.2683384
X-RAY DIFFRACTIONr_rigid_bond_restr2.27735912
X-RAY DIFFRACTIONr_sphericity_free22.1985158
X-RAY DIFFRACTIONr_sphericity_bonded9.10655926
LS refinement shellResolution: 1.221→1.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 394 -
Rwork0.254 7360 -
obs--99.86 %

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