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- PDB-8jxz: Chitin binding SusD-like protein AqSusD in complex with (GlcNAc)3 -

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Basic information

Entry
Database: PDB / ID: 8jxz
TitleChitin binding SusD-like protein AqSusD in complex with (GlcNAc)3
ComponentsSusD-like protein AqSusD
KeywordsSUGAR BINDING PROTEIN / SusD-like protein
Function / homologytriacetyl-beta-chitotriose
Function and homology information
Biological speciesAquimarina (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Structural insights of a SusD-like protein in marine Bacteroidetes bacteria reveal the molecular basis for chitin recognition and acquisition.
Authors: Yang, J. / Zhang, L. / Lin, S. / Li, W. / Liu, C. / Yan, J. / Li, S. / Long, L.
History
DepositionJul 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SusD-like protein AqSusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7952
Polymers58,1671
Non-polymers6281
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.417, 64.465, 105.274
Angle α, β, γ (deg.)90.00, 113.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

21A-885-

HOH

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Components

#1: Protein SusD-like protein AqSusD


Mass: 58166.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquimarina (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH6.5, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Dec 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→19.33 Å / Num. obs: 25384 / % possible obs: 90.37 % / Redundancy: 2.4 % / CC1/2: 0.898 / Net I/σ(I): 10.12
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 2159 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.33 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1995 7.86 %
Rwork0.186 --
obs0.1901 25381 90.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 43 374 4297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074022
X-RAY DIFFRACTIONf_angle_d0.8885488
X-RAY DIFFRACTIONf_dihedral_angle_d6.05532
X-RAY DIFFRACTIONf_chiral_restr0.052601
X-RAY DIFFRACTIONf_plane_restr0.008721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.31991160.19621395X-RAY DIFFRACTION77
2.25-2.320.24851370.18851489X-RAY DIFFRACTION81
2.32-2.380.26661200.17521496X-RAY DIFFRACTION81
2.38-2.460.29771320.19091511X-RAY DIFFRACTION83
2.46-2.550.22741320.19121550X-RAY DIFFRACTION85
2.55-2.650.25811430.19471611X-RAY DIFFRACTION87
2.65-2.770.26591370.20261659X-RAY DIFFRACTION90
2.77-2.920.25021440.19831727X-RAY DIFFRACTION93
2.92-3.10.23611420.20391789X-RAY DIFFRACTION97
3.1-3.340.24551590.19431804X-RAY DIFFRACTION99
3.34-3.670.23431570.19261838X-RAY DIFFRACTION99
3.67-4.20.21221590.16491822X-RAY DIFFRACTION99
4.2-5.270.21721550.15821855X-RAY DIFFRACTION99
5.27-19.330.20921620.19041840X-RAY DIFFRACTION97

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