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- PDB-8w4n: Crystal structure of EndoSz mutant D234M, in space group P21, in ... -

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Basic information

Entry
Database: PDB / ID: 8w4n
TitleCrystal structure of EndoSz mutant D234M, in space group P21, in complex with oligosaccharide G2S1
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / N-linked glycan / glycoside hydrolase / transglycosylation
Biological speciesStreptococcus equi subsp. zooepidemicus Sz105 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGuan, H.H. / Lin, C.C. / Hsieh, Y.C. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Jacs Au / Year: 2024
Title: Structure-Based High-Efficiency Homogeneous Antibody Platform by Endoglycosidase Sz Provides Insights into Its Transglycosylation Mechanism.
Authors: Hsieh, Y.C. / Guan, H.H. / Lin, C.C. / Huang, T.Y. / Chuankhayan, P. / Chen, N.C. / Wang, N.H. / Hu, P.L. / Tsai, Y.C. / Huang, Y.C. / Yoshimura, M. / Lin, P.J. / Hsieh, Y.H. / Chen, C.J.
History
DepositionAug 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / Item: _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: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3463
Polymers110,5761
Non-polymers1,7702
Water00
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)51.589, 101.692, 129.802
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycoside hydrolase


Mass: 110575.906 Da / Num. of mol.: 1 / Mutation: D234M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equi subsp. zooepidemicus Sz105 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1729.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-1-4-5-3-1-4/a4-b1_b3-c1_b6-g1_c2-d1_d4-e1_e6-f2_g2-h1_h4-i1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 mM sodium citrate pH 5.4 and 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→28.33 Å / Num. obs: 24061 / % possible obs: 98.23 % / Redundancy: 1.8 % / CC1/2: 0.988 / Net I/σ(I): 5
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 2397 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→28.33 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 1987 8.26 %
Rwork0.227 --
obs0.2309 24061 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 119 0 7021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037167
X-RAY DIFFRACTIONf_angle_d0.6739683
X-RAY DIFFRACTIONf_dihedral_angle_d7.8571001
X-RAY DIFFRACTIONf_chiral_restr0.0551102
X-RAY DIFFRACTIONf_plane_restr0.0031232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.3981410.34011567X-RAY DIFFRACTION98
3.18-3.260.40441360.33031585X-RAY DIFFRACTION99
3.26-3.360.38741440.29481568X-RAY DIFFRACTION99
3.36-3.470.34171430.2951567X-RAY DIFFRACTION99
3.47-3.590.38391420.28751564X-RAY DIFFRACTION98
3.59-3.730.31051340.26111559X-RAY DIFFRACTION97
3.73-3.90.26751440.25041563X-RAY DIFFRACTION98
3.9-4.110.28231420.23771564X-RAY DIFFRACTION98
4.11-4.370.25741410.21111580X-RAY DIFFRACTION99
4.37-4.70.25691450.19341577X-RAY DIFFRACTION98
4.7-5.170.23821460.19481600X-RAY DIFFRACTION99
5.17-5.910.24931430.20611562X-RAY DIFFRACTION99
5.92-7.430.24441420.20551608X-RAY DIFFRACTION99
7.43-28.330.1891440.17141610X-RAY DIFFRACTION98

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