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- PDB-6er4: Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose -

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Basic information

Entry
Database: PDB / ID: 6er4
TitleRuminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose
ComponentsBNR/Asp-box repeat protein
KeywordsSUGAR BINDING PROTEIN / sialidase / CBM / sialic acid
Function / homology
Function and homology information


exo-alpha-sialidase activity / carbohydrate metabolic process
Similarity search - Function
Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
6'-sialyl-lactose / BNR/Asp-box repeat protein
Similarity search - Component
Biological speciesRuminococcus gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsOwen, C.D. / Tailford, L.E. / Taylor, G.L. / Juge, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/F016778/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus.
Authors: Owen, C.D. / Tailford, L.E. / Monaco, S. / Suligoj, T. / Vaux, L. / Lallement, R. / Khedri, Z. / Yu, H. / Lecointe, K. / Walshaw, J. / Tribolo, S. / Horrex, M. / Bell, A. / Chen, X. / ...Authors: Owen, C.D. / Tailford, L.E. / Monaco, S. / Suligoj, T. / Vaux, L. / Lallement, R. / Khedri, Z. / Yu, H. / Lecointe, K. / Walshaw, J. / Tribolo, S. / Horrex, M. / Bell, A. / Chen, X. / Taylor, G.L. / Varki, A. / Angulo, J. / Juge, N.
History
DepositionOct 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BNR/Asp-box repeat protein
B: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7479
Polymers41,8732
Non-polymers1,8747
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The protein does not elute at a position corresponding to dimer on calibrated gel filtration column. Full length protein indicated to be a dimer by SEC MALS The ...Evidence: light scattering, The protein does not elute at a position corresponding to dimer on calibrated gel filtration column. Full length protein indicated to be a dimer by SEC MALS The crystallographic dimer, when extrapolated to the full length protein using the catalytic domain crystal structure 4X47 and 2vw2 as a scaffold would introduce substantial clashes.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint10 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.740, 72.200, 51.410
Angle α, β, γ (deg.)90.000, 103.880, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 48 - 235 / Label seq-ID: 5 - 192

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein BNR/Asp-box repeat protein / / CBM40


Mass: 20936.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus ATCC 29149 (bacteria)
Gene: RUMGNA_02694 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B557
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 6'-sialyl-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride with 20% PEG 8000 crystal growth time was improved using micro-seeding Crystals were cryoprotected using the crystallisation condition supplemented with 25% (w/w) ...Details: 0.2M ammonium chloride with 20% PEG 8000 crystal growth time was improved using micro-seeding Crystals were cryoprotected using the crystallisation condition supplemented with 25% (w/w) glycerol crystal was co-crystallised with 10mM 2,6 sialyllactose and soaked with 100mM 2,6 sialyllactose immediately prior to freezing

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.3→49.91 Å / Num. obs: 70604 / % possible obs: 83.9 % / Redundancy: 5.1 % / Rpim(I) all: 0.013 / Rrim(I) all: 0.034 / Rsym value: 0.031 / Net I/av σ(I): 14.567 / Net I/σ(I): 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRsym value% possible all
1.303-1.341.40.1485.50.1430.14813.6
1.34-1.372.40.1445.50.1190.14447.7
1.37-1.412.90.1385.80.0970.13878.7
1.41-1.4630.1087.40.0750.10881.7
1.46-1.53.10.0889.10.060.08884.6
1.5-1.563.20.07710.30.0520.07787.8
1.56-1.623.20.06312.40.0410.06390.2
1.62-1.683.60.067100.0390.06793.6
1.68-1.764.20.079.50.0370.0796
1.76-1.8450.06211.10.030.06297.6
1.84-1.946.30.05612.70.0240.05699.6
1.94-2.066.80.04216.50.0170.042100
2.06-2.26.90.03519.60.0140.035100
2.2-2.3870.03221.60.0130.032100
2.38-2.617.10.0322.20.0120.0399.9
2.61-2.917.30.02922.50.0110.029100
2.91-3.367.90.025240.010.025100
3.36-4.129.10.02523.60.0090.02599.9
4.12-5.839.70.02521.90.0090.02599.8
5.83-49.90910.10.02423.20.0080.02499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å29.23 Å
Translation1.6 Å29.23 Å

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASER2.5.6phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vw2

2vw2


Resolution: 1.3→49.91 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.194 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0505 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1345 3481 4.9 %RANDOM
Rwork0.1084 ---
obs0.1097 67097 83.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 93.54 Å2 / Biso mean: 11.479 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0.37 Å2
2---0.16 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.3→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 123 488 3507
Biso mean--14.22 27.41 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193274
X-RAY DIFFRACTIONr_bond_other_d0.0080.023105
X-RAY DIFFRACTIONr_angle_refined_deg1.7122.0024433
X-RAY DIFFRACTIONr_angle_other_deg1.6537196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1935428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24625.396139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4171516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023772
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02698
X-RAY DIFFRACTIONr_mcbond_it0.7710.8751649
X-RAY DIFFRACTIONr_mcbond_other0.7650.8751648
X-RAY DIFFRACTIONr_mcangle_it1.0341.3152098
X-RAY DIFFRACTIONr_rigid_bond_restr2.37536376
X-RAY DIFFRACTIONr_sphericity_free31.8025105
X-RAY DIFFRACTIONr_sphericity_bonded7.21556701
Refine LS restraints NCS

Ens-ID: 1 / Number: 22806 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 46 -
Rwork0.205 793 -
all-839 -
obs--13.53 %

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