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- PDB-4x47: Crystal structure of the intramolecular trans-sialidase from Rumi... -

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Basic information

Entry
Database: PDB / ID: 4x47
TitleCrystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Neu5Ac2en
ComponentsAnhydrosialidase
KeywordsHYDROLASE / intramolecular / trans-sialidase / sialidase / neuraminidase / neu5Ac2en / DANA / inhibitor / complex / anhydrosialidase
Function / homology
Function and homology information


exo-alpha-sialidase activity / carbohydrate metabolic process
Similarity search - Function
Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily ...Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / PHOSPHATE ION / Anhydrosialidase
Similarity search - Component
Biological speciesRuminococcus gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsOwen, C.D. / Tailford, L.E. / Taylor, G.L. / Juge, N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004529/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L008602/1 United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation.
Authors: Tailford, L.E. / Owen, C.D. / Walshaw, J. / Crost, E.H. / Hardy-Goddard, J. / Le Gall, G. / de Vos, W.M. / Taylor, G.L. / Juge, N.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / 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 / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Nov 21, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Jan 10, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anhydrosialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3793
Polymers53,9931
Non-polymers3862
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-5 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.305, 101.305, 131.939
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Anhydrosialidase


Mass: 53992.605 Da / Num. of mol.: 1 / Fragment: UNP residues 243-723
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus ATCC 29149 (bacteria)
Gene: HMPREF1201_01421 / Production host: Escherichia coli (E. coli) / References: UniProt: V8BWT1, exo-alpha-sialidase
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: microseeding into 0.8 M NaH2PO4, 1.2M K2HPO4, sodium acetate 0.1M pH 4.5

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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: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 33968 / % possible obs: 99.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.064 / Χ2: 2.572 / Net I/av σ(I): 25.422 / Net I/σ(I): 15.3 / Num. measured all: 97905
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.032.60.4917432.36499.7
2.03-2.072.90.43316722.43999.8
2.07-2.112.90.39217302.4299.9
2.11-2.152.90.33917072.451100
2.15-2.22.90.34416812.35799.9
2.2-2.252.80.33917042.48199.8
2.25-2.312.80.30117122.3899.5
2.31-2.372.70.29616922.51299.5
2.37-2.442.70.23317112.60799.4
2.44-2.522.70.21216802.57298.9
2.52-2.612.70.1816782.62699
2.61-2.712.80.1616922.69899.4
2.71-2.842.80.12316862.72799.2
2.84-2.992.90.09417042.90899.5
2.99-3.1730.07217173.10699.8
3.17-3.423.10.05516923.15299.9
3.42-3.763.10.04517012.959100
3.76-4.3130.03517002.27798.8
4.31-5.4330.02916761.95299.1
5.43-453.10.03116902.33498.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å21.64 Å
Translation2 Å21.64 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2sli

2sli


Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2471 / WRfactor Rwork: 0.1934 / FOM work R set: 0.7082 / SU B: 7.093 / SU ML: 0.185 / SU R Cruickshank DPI: 0.2221 / SU Rfree: 0.1982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 1586 4.7 %RANDOM
Rwork0.2146 32166 --
obs0.2174 32166 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.63 Å2 / Biso mean: 40.44 Å2 / Biso min: 20.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å20 Å2
2--1.11 Å20 Å2
3----3.61 Å2
Refinement stepCycle: final / Resolution: 2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 25 235 4063
Biso mean--39.02 43.51 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023934
X-RAY DIFFRACTIONr_bond_other_d0.0010.023555
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9575342
X-RAY DIFFRACTIONr_angle_other_deg0.82938229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39325.385182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03515640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5961511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02887
X-RAY DIFFRACTIONr_mcbond_it3.4813.971965
X-RAY DIFFRACTIONr_mcbond_other3.4813.971964
X-RAY DIFFRACTIONr_mcangle_it4.5445.9422458
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 130 -
Rwork0.335 2380 -
all-2510 -
obs--99.6 %

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