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- PDB-8j30: Crystal structure of ApNGT with Q469A and M218A mutations in comp... -

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Basic information

Entry
Database: PDB / ID: 8j30
TitleCrystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-GLC
ComponentsUDP-glucose:protein N-beta-glucosyltransferase
KeywordsTRANSFERASE / Actinobacillus pleuropneumoniae / N-glycosyltransferase
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Hexosyltransferases / : / glycosyltransferase activity / cytoplasm
Similarity search - Function
HMW1 domain 2 / HMW1C N-terminal / HMW1C N-terminal / HMW1 domain 2 / :
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose:protein N-beta-glucosyltransferase
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae serovar 5b str. L20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsFeng, Y. / Hao, Z. / Guo, Q. / Zheng, J. / Da, L. / Peng, W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91853121 China
National Natural Science Foundation of China (NSFC)21977066 China
National Natural Science Foundation of China (NSFC)22177069 China
National Natural Science Foundation of China (NSFC)22177072 China
CitationJournal: Jacs Au / Year: 2023
Title: Investigation of the Catalytic Mechanism of a Soluble N-glycosyltransferase Allows Synthesis of N-glycans at Noncanonical Sequons.
Authors: Hao, Z. / Guo, Q. / Feng, Y. / Zhang, Z. / Li, T. / Tian, Z. / Zheng, J. / Da, L.T. / Peng, W.
History
DepositionApr 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose:protein N-beta-glucosyltransferase
B: UDP-glucose:protein N-beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0354
Polymers143,0642
Non-polymers9702
Water00
1
A: UDP-glucose:protein N-beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0992
Polymers71,5321
Non-polymers5661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose:protein N-beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9362
Polymers71,5321
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.409, 95.011, 175.974
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 UDP-glucose:protein N-beta-glucosyltransferase / UDP-Glc:protein N-glucosyltransferase / HMW1C-like protein / N-glycosyltransferase / NGT


Mass: 71532.242 Da / Num. of mol.: 2 / Mutation: Q469A,M218A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae serovar 5b str. L20 (bacteria)
Gene: APL_1635 / Production host: Escherichia coli (E. coli)
References: UniProt: A3N2T3, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / 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
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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TBis-Tris-HCl (pH 6.5), 2%(v/v) Tacsimate(pH 6.0), 20%(v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 30111 / % possible obs: 98.78 % / Redundancy: 6.2 % / CC1/2: 0.985 / Net I/σ(I): 13.9
Reflection shellResolution: 2.88→2.93 Å / Num. unique obs: 28618 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→47.18 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1527 5.07 %RANDOM
Rwork0.2114 ---
obs0.2134 30111 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9627 0 61 0 9688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.273
X-RAY DIFFRACTIONf_dihedral_angle_d5.6191303
X-RAY DIFFRACTIONf_chiral_restr0.071490
X-RAY DIFFRACTIONf_plane_restr0.0081735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.990.36941160.27352533X-RAY DIFFRACTION97
2.99-3.090.30641410.27382535X-RAY DIFFRACTION99
3.09-3.220.33681400.26212579X-RAY DIFFRACTION99
3.22-3.360.28621320.25452592X-RAY DIFFRACTION100
3.36-3.540.25371300.23792595X-RAY DIFFRACTION99
3.54-3.760.31111530.21332534X-RAY DIFFRACTION97
3.76-4.050.24321550.20322579X-RAY DIFFRACTION100
4.05-4.460.22291370.18312633X-RAY DIFFRACTION100
4.46-5.10.1981330.18252638X-RAY DIFFRACTION99
5.1-6.430.24531460.20472619X-RAY DIFFRACTION98
6.43-7.810.19261440.18532747X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 12.038 Å / Origin y: 24.4499 Å / Origin z: 18.5959 Å
111213212223313233
T0.1727 Å20.0067 Å20.0018 Å2-0.1709 Å20.0277 Å2--0.1652 Å2
L0.0204 °20.0767 °20.0267 °2-0.1724 °20.1054 °2--0.0314 °2
S0.0023 Å °0.0016 Å °-0.0029 Å °0.0404 Å °-0.006 Å °0.0542 Å °0.0049 Å °0.0077 Å °-0 Å °
Refinement TLS groupSelection details: all

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