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- PDB-8p0p: Crystal structure of AaNGT complexed to UDP-2F-Glucose -

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Basic information

Entry
Database: PDB / ID: 8p0p
TitleCrystal structure of AaNGT complexed to UDP-2F-Glucose
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 / Chem-U2F / URIDINE-5'-DIPHOSPHATE / Adhesin
Function and homology information
Biological speciesAggregatibacter aphrophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsPiniello, 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)142,7064
Polymers141,7332
Non-polymers9722
Water1448
1
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4352
Polymers70,8671
Non-polymers5681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2712
Polymers70,8671
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.068, 114.005, 258.008
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-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: calcium acetate, sodium acetate, 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: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.73→258.01 Å / Num. obs: 38131 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 8.7
Reflection shellResolution: 2.73→2.88 Å / Num. unique obs: 5436 / CC1/2: 0.458

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→129 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 46.244 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24517 1430 3.8 %RANDOM
Rwork0.19704 ---
obs0.19883 36614 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.711 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20 Å2
2--3.62 Å2-0 Å2
3----3.21 Å2
Refinement stepCycle: 1 / Resolution: 2.73→129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9966 0 61 8 10035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01210272
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169569
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.6513952
X-RAY DIFFRACTIONr_angle_other_deg0.4521.57222042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12951242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.921558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.737101732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022400
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_it6.9097.5244974
X-RAY DIFFRACTIONr_mcbond_other6.9077.5254974
X-RAY DIFFRACTIONr_mcangle_it10.28513.5336214
X-RAY DIFFRACTIONr_mcangle_other10.28813.5346215
X-RAY DIFFRACTIONr_scbond_it6.6767.8125298
X-RAY DIFFRACTIONr_scbond_other6.6547.8045291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.2214.2427739
X-RAY DIFFRACTIONr_long_range_B_refined12.83369.7511336
X-RAY DIFFRACTIONr_long_range_B_other12.83269.7511337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 105 -
Rwork0.394 2669 -
obs--99.93 %
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)
10.41510.0270.0950.93850.08810.2970.01560.0626-0.12610.2547-0.10240.1353-0.1319-0.08620.08680.38460.05210.01170.3621-0.09380.1925-5.3924-8.813558.442
20.38660.1063-0.23420.3254-0.0080.79340.08860.3959-0.12590.033-0.13750.0527-0.3694-0.11060.04890.38030.0673-0.07760.7905-0.2050.09461.5241-0.01416.2684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 804
2X-RAY DIFFRACTION2B0 - 804

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