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- PDB-6n1a: Crystal structure of an N-acetylgalactosamine deacetylase from F.... -

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Basic information

Entry
Database: PDB / ID: 6n1a
TitleCrystal structure of an N-acetylgalactosamine deacetylase from F. plautii
ComponentsCarbohydrate-binding protein
KeywordsHYDROLASE / N-acetylgalactosamine deacetylase / A Blood antigen / CAZy
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metabolic process
Similarity search - Function
Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Sialidase superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
: / Carbohydrate-binding protein / F5/8 type C domain protein
Similarity search - Component
Biological speciesFlavonifractor plautii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSim, L. / Rahfeld, P. / Withers, S.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-136940 Canada
CitationJournal: Nat Microbiol / Year: 2019
Title: An enzymatic pathway in the human gut microbiome that converts A to universal O type blood.
Authors: Rahfeld, P. / Sim, L. / Moon, H. / Constantinescu, I. / Morgan-Lang, C. / Hallam, S.J. / Kizhakkedathu, J.N. / Withers, S.G.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2487
Polymers55,8371
Non-polymers4116
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.584, 69.186, 104.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbohydrate-binding protein / N-acetylgalactosamine deacetylase


Mass: 55836.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavonifractor plautii (bacteria) / Gene: A4U99_12080 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1C7FP65, UniProt: G9YSP4*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.67 Å3/Da / Density % sol: 26.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M CaCl2, 0.1 M MES pH 6.0, 18% PEG 4000, and 20 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9194 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 1.6→46.2 Å / Num. obs: 48937 / % possible obs: 97.7 % / Redundancy: 22.9 % / CC1/2: 1 / Rpim(I) all: 0.02 / Net I/av σ(I): 27.4 / Net I/σ(I): 27.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1932 / CC1/2: 0.63 / Rpim(I) all: 0.4 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→46.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1666 2406 4.9 %RANDOM
Rwork0.1388 ---
obs0.1402 46465 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.72 Å2 / Biso mean: 19.049 Å2 / Biso min: 1.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.6→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 21 365 3456
Biso mean--34.78 29.99 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023207
X-RAY DIFFRACTIONr_bond_other_d00.022696
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.934389
X-RAY DIFFRACTIONr_angle_other_deg3.81236282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2425395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76224.62171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67515459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.351518
X-RAY DIFFRACTIONr_chiral_restr0.1330.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213680
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02686
X-RAY DIFFRACTIONr_mcbond_it1.5071.7171553
X-RAY DIFFRACTIONr_mcbond_other1.5061.7161552
X-RAY DIFFRACTIONr_mcangle_it2.0862.5721942
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 139 -
Rwork0.237 2765 -
all-2904 -
obs--79.98 %

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