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- PDB-6er2: Ruminococcus gnavus IT-sialidase CBM40 -

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Basic information

Entry
Database: PDB / ID: 6er2
TitleRuminococcus gnavus IT-sialidase CBM40
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
Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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 ...Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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
BNR/Asp-box repeat protein
Similarity search - Component
Biological speciesRuminococcus gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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


Theoretical massNumber of molelcules
Total (without water)41,0122
Polymers41,0122
Non-polymers00
Water6,089338
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 slashes.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-5 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.683, 72.745, 51.292
Angle α, β, γ (deg.)90.000, 104.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 8 - 194 / Label seq-ID: 2 - 188

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

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Components

#1: Protein BNR/Asp-box repeat protein / RgCBM40


Mass: 20505.947 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride with 20% PEG 8000 The drop contained 0.5 microlitre protein solution at 25 mg/ml and 0.5 microlitre reservoir solution

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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 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 33276 / % possible obs: 91.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.034 / Χ2: 1.862 / Net I/av σ(I): 47.293 / Net I/σ(I): 30.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.73-1.762.40.142.064151.3
1.76-1.792.50.1272.234162.1
1.79-1.832.70.1152.243171
1.83-1.862.90.1062.239182
1.86-1.93.40.0942.172194.2
1.9-1.953.80.0872.176196.9
1.95-23.80.0712.167196.6
2-2.053.80.062.027197.1
2.05-2.113.90.0541.972197
2.11-2.183.90.0481.843197.8
2.18-2.263.90.0431.784197.9
2.26-2.3540.041.748198.1
2.35-2.4540.0381.682198.8
2.45-2.583.90.0361.666199.1
2.58-2.7540.0321.514199.1
2.75-2.9640.0291.485199.5
2.96-3.2640.0281.508199.6
3.26-3.7340.0271.645199.5
3.73-4.6940.0291.823199.4
4.69-503.90.0312.216197.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.95 Å20.67 Å
Translation1.95 Å20.67 Å

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vw2

2vw2


Resolution: 1.73→49.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.015 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1698 5.1 %RANDOM
Rwork0.1596 ---
obs0.1614 31570 91.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 101.18 Å2 / Biso mean: 19.986 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0.92 Å2
2--0.49 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 1.73→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 0 338 3126
Biso mean---28.11 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192841
X-RAY DIFFRACTIONr_bond_other_d0.0060.022716
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9653830
X-RAY DIFFRACTIONr_angle_other_deg1.25536254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7985369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54825.469128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4151514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023283
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02619
X-RAY DIFFRACTIONr_mcbond_it2.0741.6771482
X-RAY DIFFRACTIONr_mcbond_other2.0721.6761481
X-RAY DIFFRACTIONr_mcangle_it2.862.4951849
Refine LS restraints NCS

Ens-ID: 1 / Number: 21944 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.727→1.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 78 -
Rwork0.222 1308 -
all-1386 -
obs--51.77 %

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