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- PDB-8p0o: Crystal structure of AaNGT complexed to UDP-Gal -

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Basic information

Entry
Database: PDB / ID: 8p0o
TitleCrystal structure of AaNGT complexed to UDP-Gal
ComponentsAdhesin
KeywordsTRANSFERASE / N-glycosylation / Asn tautomeric form / AAD / Glycosyltransferase / GT-B
Function / homologyHMW1 domain 2 / HMW1C N-terminal / HMW1C N-terminal / HMW1 domain 2 / glycosyltransferase activity / GALACTOSE-URIDINE-5'-DIPHOSPHATE / Adhesin
Function and homology information
Biological speciesAggregatibacter aphrophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsPinello, B. / Macias-Leon, J. / Rovira, C. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2019-105451GB-I00 Spain
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis for bacterial N-glycosylation by a soluble HMW1C-like N-glycosyltransferase.
Authors: Piniello, B. / Macias-Leon, J. / Miyazaki, S. / Garcia-Garcia, A. / Companon, I. / Ghirardello, M. / Taleb, V. / Veloz, B. / Corzana, F. / Miyagawa, A. / Rovira, C. / Hurtado-Guerrero, R.
History
DepositionMay 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin
B: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,48030
Polymers141,7332
Non-polymers2,74628
Water14,070781
1
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,24015
Polymers70,8671
Non-polymers1,37314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,24015
Polymers70,8671
Non-polymers1,37314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.338, 113.331, 260.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adhesin


Mass: 70866.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter aphrophilus (bacteria) / Gene: DOL88_00785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3M6PNT1
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: magnesium chloride, HEPES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→20 Å / Num. obs: 139852 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.2
Reflection shellResolution: 1.76→1.86 Å / Rmerge(I) obs: 1.796 / Num. unique obs: 20146 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.923 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20714 5578 4 %RANDOM
Rwork0.17434 ---
obs0.17568 134160 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20 Å2
2--0.12 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10134 0 0 781 10915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01210354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169695
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.65514011
X-RAY DIFFRACTIONr_angle_other_deg0.4891.57222323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2351241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.832558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.862101730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21556
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022399
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6663.0214970
X-RAY DIFFRACTIONr_mcbond_other2.6613.0214969
X-RAY DIFFRACTIONr_mcangle_it3.5325.4186209
X-RAY DIFFRACTIONr_mcangle_other3.5325.4196210
X-RAY DIFFRACTIONr_scbond_it4.0333.4965384
X-RAY DIFFRACTIONr_scbond_other4.0333.4965385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.946.1967803
X-RAY DIFFRACTIONr_long_range_B_refined7.2131.3711756
X-RAY DIFFRACTIONr_long_range_B_other7.18230.7511613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 393 -
Rwork0.336 9707 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1532-0.1489-0.07610.19060.09440.2796-0.05030.0164-0.04470.0830.02320.0329-0.03020.01620.02720.06370.02160.00010.0358-0.0210.0682-5.889-9.25658.309
20.0984-0.0618-0.17530.2581-0.08320.5430.08820.0488-0.0541-0.0353-0.14540.0389-0.17390.00440.05720.08410.0339-0.05180.087-0.0270.05051.435-0.4226.22
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 621
2X-RAY DIFFRACTION1A801 - 814
3X-RAY DIFFRACTION2B0 - 620
4X-RAY DIFFRACTION2B801 - 814

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