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- PDB-8x8g: Crystal structure of EndoSz mutant D234M, from Streptococcus equi... -

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Basic information

Entry
Database: PDB / ID: 8x8g
TitleCrystal structure of EndoSz mutant D234M, from Streptococcus equi subsp. Zooepidemicus Sz105, in complex with oligosaccharide G2S2-oxazoline
Componentsglycoside hydrolase
KeywordsHYDROLASE / N-linked glycan / glycoside hydrolase / transglycosylation / G2S2-oxazoline
Function / homology: / Chem-NGO
Function and homology information
Biological speciesStreptococcus equi subsp. zooepidemicus Sz105 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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
DepositionNov 27, 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

Downloads & links

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Assembly

Deposited unit
A: glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6814
Polymers107,6201
Non-polymers2,0623
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.061, 232.603, 50.654
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 glycoside hydrolase


Mass: 107619.539 Da / Num. of mol.: 1
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)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide, Oligosaccharide / Mass: 1817.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: BIRD: PRD_002420
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4-5-2-3-4-5/a3-b1_a6-f1_b2-c1_c4-d1_d6-e2_f2-g1_g4-h1_h6-i2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{[(6+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NGO / 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE / N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE


Type: Oligosaccharide / Mass: 204.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14NO5 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002420
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: sodium HEPES (0.1 M, pH 7.5) and sodium citrate tribasic (1.4M)

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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: 2.27→46.44 Å / Num. obs: 56140 / % possible obs: 99.58 % / Redundancy: 3.2 % / CC1/2: 0.995 / Net I/σ(I): 6.3
Reflection shellResolution: 2.27→2.35 Å / Num. unique obs: 5550 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→46.44 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 2846 5.07 %
Rwork0.2075 --
obs0.2096 56113 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 138 294 7334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057173
X-RAY DIFFRACTIONf_angle_d0.9179692
X-RAY DIFFRACTIONf_dihedral_angle_d6.571027
X-RAY DIFFRACTIONf_chiral_restr0.0521096
X-RAY DIFFRACTIONf_plane_restr0.0061232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.310.31131480.26762666X-RAY DIFFRACTION100
2.31-2.350.27261450.25932611X-RAY DIFFRACTION100
2.35-2.40.3091280.25282631X-RAY DIFFRACTION100
2.4-2.450.35641260.25352613X-RAY DIFFRACTION100
2.45-2.50.34621470.25162639X-RAY DIFFRACTION100
2.5-2.560.30041480.25432647X-RAY DIFFRACTION100
2.56-2.620.31531300.2442636X-RAY DIFFRACTION100
2.62-2.690.28811370.23732662X-RAY DIFFRACTION100
2.69-2.770.25311260.23692639X-RAY DIFFRACTION100
2.77-2.860.25971640.23222624X-RAY DIFFRACTION100
2.86-2.960.24791310.23162670X-RAY DIFFRACTION100
2.96-3.080.33761350.23542640X-RAY DIFFRACTION100
3.08-3.220.32671470.22942654X-RAY DIFFRACTION100
3.22-3.390.28471390.21812688X-RAY DIFFRACTION100
3.39-3.60.2481240.20442677X-RAY DIFFRACTION99
3.6-3.880.23581400.19322665X-RAY DIFFRACTION99
3.88-4.270.2171490.17272661X-RAY DIFFRACTION99
4.27-4.890.19431500.16222679X-RAY DIFFRACTION99
4.89-6.160.20871650.19142720X-RAY DIFFRACTION99
6.16-46.440.21981670.20042845X-RAY DIFFRACTION98

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