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- PDB-8p0q: Crystal structure of AaNGT complexed to UDP and a peptide -

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Basic information

Entry
Database: PDB / ID: 8p0q
TitleCrystal structure of AaNGT complexed to UDP and a peptide
Components
  • Adhesin
  • PHE-GLY-ASN-TRP-THR-THR
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 / URIDINE-5'-DIPHOSPHATE / Adhesin
Function and homology information
Biological speciesAggregatibacter aphrophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

Downloads & links

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Assembly

Deposited unit
A: Adhesin
B: Adhesin
C: PHE-GLY-ASN-TRP-THR-THR
D: PHE-GLY-ASN-TRP-THR-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8776
Polymers143,0694
Non-polymers8082
Water905
1
A: Adhesin
C: PHE-GLY-ASN-TRP-THR-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9393
Polymers71,5342
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area23950 Å2
MethodPISA
2
B: Adhesin
D: PHE-GLY-ASN-TRP-THR-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9393
Polymers71,5342
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-11 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.025, 111.477, 256.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 616 / Label seq-ID: 1 - 616

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Adhesin


Mass: 70809.672 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: Protein/peptide PHE-GLY-ASN-TRP-THR-THR


Mass: 724.761 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: It is a peptide / Source: (synth.) Aggregatibacter aphrophilus (bacteria)
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / 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.: 5 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: polyacrylic acid 5,100 sodium salt, HEPES sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 34243 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.177 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 4940 / CC1/2: 0.352

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 37.268 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23722 1344 3.9 %RANDOM
Rwork0.1785 ---
obs0.18091 32753 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.251 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20 Å2
2--5.32 Å20 Å2
3----2.87 Å2
Refinement stepCycle: 1 / Resolution: 2.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9998 0 50 5 10053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310295
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179348
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.64113983
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5721715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5851241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40322.693557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.396151734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0981558
X-RAY DIFFRACTIONr_chiral_restr0.0720.21359
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022182
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_it3.8946.4974976
X-RAY DIFFRACTIONr_mcbond_other3.8916.4974975
X-RAY DIFFRACTIONr_mcangle_it5.9869.7536213
X-RAY DIFFRACTIONr_mcangle_other5.9869.7536214
X-RAY DIFFRACTIONr_scbond_it4.0946.8375319
X-RAY DIFFRACTIONr_scbond_other4.0946.8375320
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.42510.1097771
X-RAY DIFFRACTIONr_long_range_B_refined8.85574.88111197
X-RAY DIFFRACTIONr_long_range_B_other8.85474.88711198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19545 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 94 -
Rwork0.329 2344 -
obs--99.19 %
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)
10.14690.07170.10580.393-0.10590.21060.01340.0508-0.06240.13150.00750.0924-0.1174-0.0113-0.02090.2550.0611-0.01330.123-0.02890.2457-5.8921-6.907257.9611
20.07110.02-0.19230.6834-0.33211.13420.12110.0588-0.07490.0199-0.16340.1242-0.36130.03030.04230.22860.0941-0.10620.3169-0.07340.14911.38250.99586.3033
31.09674.2312.722722.049911.01496.8114-0.0777-0.11480.0565-0.4541-0.0171-0.6083-0.2161-0.22590.09480.20640.0508-0.01280.16680.01650.25770.6807-5.926359.3167
444.0052-10.33860.36037.6873-2.76211.37750.1962-1.32381.9437-1.0718-0.6351-1.35580.57970.39210.43890.5241-0.25010.05690.7870.30030.3722-4.2617-0.14885.2181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 701
2X-RAY DIFFRACTION2B1 - 701
3X-RAY DIFFRACTION3C1 - 6
4X-RAY DIFFRACTION4D4 - 6

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