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- PDB-8w4i: Crystal structure of EndoSz mutant D234M in space group P21 -

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Basic information

Entry
Database: PDB / ID: 8w4i
TitleCrystal structure of EndoSz mutant D234M in space group P21
Componentsglycoside hydrolase
KeywordsHYDROLASE / N-linked glycan / glycoside hydrolase / transglycosylation
Biological speciesStreptococcus equi subsp. zooepidemicus Sz105 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.412, 101.716, 129.243
Angle α, β, γ (deg.)90.000, 90.370, 90.000
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: 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M 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: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→28.3 Å / Num. obs: 29373 / % possible obs: 99.53 % / Redundancy: 2 % / CC1/2: 0.991 / Net I/σ(I): 8.4
Reflection shellResolution: 2.91→3.01 Å / Num. unique obs: 2912 / CC1/2: 0.592

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.3 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2725 2002 6.82 %
Rwork0.2293 27363 -
obs0.2323 29365 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.27 Å2 / Biso mean: 69.7085 Å2 / Biso min: 20.07 Å2
Refinement stepCycle: final / Resolution: 2.9→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 1 0 6903
Biso mean--90.68 --
Num. residues----866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.980.34371420.31391912205499
2.98-3.060.36261460.300419372083100
3.06-3.150.33271410.295619542095100
3.15-3.250.2831420.279519692111100
3.25-3.360.35521450.285319402085100
3.36-3.50.35861430.259819372080100
3.5-3.660.33741360.245719762112100
3.66-3.850.27221430.22951912205599
3.85-4.090.24781410.20671963210499
4.09-4.410.24611460.193819642110100
4.41-4.850.23191440.19319402084100
4.85-5.540.25941440.210619742118100
5.54-6.970.28751400.232319722112100
6.97-28.30.20471490.20362013216299

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