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- PDB-8u2a: Crystal structure of NanI in complex with Neu5,9Ac -

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Basic information

Entry
Database: PDB / ID: 8u2a
TitleCrystal structure of NanI in complex with Neu5,9Ac
ComponentsExo-alpha-sialidase
KeywordsHYDROLASE / Complex / Glycoside Hydrolase / sialic acid
Function / homologyChem-5N6 / NITRATE ION / :
Function and homology information
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMedley, B.J. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Glycomics Network (GLYCONET) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A "terminal" case of glycan catabolism: Structural and enzymatic characterization of the sialidases of Clostridium perfringens.
Authors: Medley, B.J. / Low, K.E. / Irungu, J.D.W. / Kipchumba, L. / Daneshgar, P. / Liu, L. / Garber, J.M. / Klassen, L. / Inglis, G.D. / Boons, G.J. / Zandberg, W.F. / Abbott, D.W. / Boraston, A.B.
History
DepositionSep 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.title / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5856
Polymers50,0631
Non-polymers5215
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.482, 72.331, 97.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Exo-alpha-sialidase


Mass: 50063.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria)
Gene: nanI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z3TZA2
#5: Sugar ChemComp-5N6 / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / (2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca rboxylic acid / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 351.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21NO10 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Neup5Ac9AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 165 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 15mM Neu5Ac, 20% PEG 3350, 0.2M KNO3, ph 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 33504 / % possible obs: 97.8 % / Redundancy: 5.1 % / CC1/2: 0.982 / Rpim(I) all: 0.064 / Rrim(I) all: 0.158 / Net I/σ(I): 11
Reflection shellResolution: 1.99→2 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1509 / CC1/2: 0.791 / Rpim(I) all: 0.261 / Rrim(I) all: 0.452 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→19.93 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1577 4.86 %
Rwork0.2122 --
obs0.2141 32466 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 34 161 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083601
X-RAY DIFFRACTIONf_angle_d0.9684879
X-RAY DIFFRACTIONf_dihedral_angle_d7.216488
X-RAY DIFFRACTIONf_chiral_restr0.061527
X-RAY DIFFRACTIONf_plane_restr0.007640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.050.3087920.24752343X-RAY DIFFRACTION79
2.05-2.130.29811190.25792684X-RAY DIFFRACTION91
2.13-2.210.38331590.29752680X-RAY DIFFRACTION92
2.21-2.310.34571530.32672680X-RAY DIFFRACTION92
2.31-2.430.30341630.24932854X-RAY DIFFRACTION97
2.43-2.590.25721500.22922886X-RAY DIFFRACTION98
2.59-2.780.24981420.2262903X-RAY DIFFRACTION98
2.79-3.060.28211390.22582910X-RAY DIFFRACTION98
3.06-3.510.28221340.212956X-RAY DIFFRACTION98
3.51-4.410.20571440.17992930X-RAY DIFFRACTION97
4.41-19.930.17261820.14783063X-RAY DIFFRACTION98

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