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- PDB-4x4a: Crystal structure of the intramolecular trans-sialidase from Rumi... -

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Basic information

Entry
Database: PDB / ID: 4x4a
TitleCrystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with 2,7-Anhydro-Neu5Ac
ComponentsAnhydrosialidase
KeywordsHYDROLASE / intramolecular / trans-sialidase / sialidase / neuraminidase / 2-7-anhydro-neu5ac / reaction product / anhydrosialdiase
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
ACETYL GROUP / PHOSPHATE ION / Chem-SKD / Anhydrosialidase
Similarity search - Component
Biological speciesRuminococcus gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 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_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_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_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_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 2.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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)54,6997
Polymers53,9931
Non-polymers7076
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.257, 99.257, 130.599
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 535 molecules

#2: Chemical ChemComp-SKD / 2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID / 2,7-ANHYDRO-NEU5AC


Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: micro seeding 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 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.71→45 Å / Num. obs: 48126 / % possible obs: 92.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.049 / Χ2: 2.351 / Net I/av σ(I): 41.73 / Net I/σ(I): 20 / Num. measured all: 201356
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.71-1.742.40.42113581.96553
1.74-1.772.60.43215992.10661.9
1.77-1.812.90.35118422.08371
1.81-1.843.10.30321042.09981
1.84-1.883.60.28223832.22592.8
1.88-1.934.20.23425952.251100
1.93-1.974.30.19226132.332100
1.97-2.034.30.15625792.444100
2.03-2.094.30.13725612.475100
2.09-2.154.40.11326242.494100
2.15-2.234.40.10125592.513100
2.23-2.324.40.09226342.521100
2.32-2.434.40.0825902.43999.9
2.43-2.554.50.07225702.534100
2.55-2.714.50.06325712.408100
2.71-2.924.60.05326222.389100
2.92-3.224.60.04425982.316100
3.22-3.684.70.03625612.16899.9
3.68-4.644.60.03225952.167100
4.64-454.70.03325682.30398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.71 Å18.76 Å
Translation1.71 Å18.76 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 / Resolution: 1.71→45 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2024 / WRfactor Rwork: 0.1592 / FOM work R set: 0.8168 / SU B: 2.42 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1118 / SU Rfree: 0.1121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2250 4.7 %RANDOM
Rwork0.1432 45702 --
obs0.1454 45702 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.4 Å2 / Biso mean: 29.958 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 1.71→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 46 529 4354
Biso mean--37.19 44.62 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023972
X-RAY DIFFRACTIONr_bond_other_d0.0010.023589
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.965397
X-RAY DIFFRACTIONr_angle_other_deg0.88338308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7815497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16925.459185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38815644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2511511
X-RAY DIFFRACTIONr_chiral_restr0.1220.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02898
X-RAY DIFFRACTIONr_mcbond_it2.5162.7551974
X-RAY DIFFRACTIONr_mcbond_other2.5152.7561975
X-RAY DIFFRACTIONr_mcangle_it3.2384.1212475
LS refinement shellResolution: 1.71→1.755 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 86 -
Rwork0.264 2015 -
all-2101 -
obs--54.96 %

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