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- PDB-8w4g: Crystal structure of EndoSz mutant D234M, from Streptococcus equi... -

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Basic information

Entry
Database: PDB / ID: 8w4g
TitleCrystal structure of EndoSz mutant D234M, from Streptococcus equi subsp. Zooepidemicus Sz105
Componentsglycoside hydrolase
KeywordsHYDROLASE / N-linked glycan / glycoside hydrolase / transglycosylation
Biological speciesStreptococcus equi subsp. zooepidemicus Sz105 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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)110,6162
Polymers110,5761
Non-polymers401
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area42640 Å2
Unit cell
Length a, b, c (Å)50.947, 101.207, 234.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium HEPES pH 7.5 and 1.4 M sodium citrate tribasic

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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: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→42.57 Å / Num. obs: 66610 / % possible obs: 99.11 % / Redundancy: 3.2 % / CC1/2: 0.995 / Net I/σ(I): 6.8
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 6627 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→42.57 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 3139 4.72 %
Rwork0.2149 63416 -
obs0.2165 66555 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 277.39 Å2 / Biso mean: 57.3585 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 2.15→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 1 441 7344
Biso mean--83.73 50.27 -
Num. residues----876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.180.31041430.299428522995100
2.18-2.220.35111690.31128693038100
2.22-2.260.3031150.285528482963100
2.26-2.30.31041400.283628803020100
2.3-2.340.32971530.281228322985100
2.34-2.390.31621220.274828983020100
2.39-2.440.26251560.25952841299799
2.44-2.50.31671480.24522831297999
2.5-2.560.29131500.248328903040100
2.56-2.630.30251320.254428592991100
2.63-2.710.29341430.24242883302699
2.71-2.80.25781400.254328522992100
2.8-2.90.31551420.24982884302699
2.9-3.010.26341410.23862885302699
3.01-3.150.26731390.24252866300599
3.15-3.310.25351360.22292869300599
3.32-3.520.2431440.21562882302699
3.52-3.790.21411380.19062862300098
3.79-4.180.21421460.18022874302098
4.18-4.780.23381430.16792906304998
4.78-6.020.20861470.18012942308998
6.02-42.570.22061520.18813111326398

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