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- PDB-8qx6: Novel laminarin-binding CBM X584 -

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Basic information

Entry
Database: PDB / ID: 8qx6
TitleNovel laminarin-binding CBM X584
ComponentsPKD domain-containing protein
KeywordsSUGAR BINDING PROTEIN / CBM X584 / Surface glycan binding protein / carbohydrate binding module / ligand complex
Function / homologyPolycystic kidney disease (PKD) domain profile. / PKD domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / PKD domain-containing protein
Function and homology information
Biological speciesChristiangramia forsetii KT0803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZuehlke, M.K. / Jeudy, A. / Czjzek, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR 2406 Germany
CitationJournal: Environ.Microbiol. / Year: 2024
Title: Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms.
Authors: Zuhlke, M.K. / Ficko-Blean, E. / Bartosik, D. / Terrapon, N. / Jeudy, A. / Jam, M. / Wang, F. / Welsch, N. / Durwald, A. / Martin, L.T. / Larocque, R. / Jouanneau, D. / Eisenack, T. / ...Authors: Zuhlke, M.K. / Ficko-Blean, E. / Bartosik, D. / Terrapon, N. / Jeudy, A. / Jam, M. / Wang, F. / Welsch, N. / Durwald, A. / Martin, L.T. / Larocque, R. / Jouanneau, D. / Eisenack, T. / Thomas, F. / Trautwein-Schult, A. / Teeling, H. / Becher, D. / Schweder, T. / Czjzek, M.
History
DepositionOct 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PKD domain-containing protein
B: PKD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1944
Polymers36,1852
Non-polymers1,0092
Water1,63991
1
A: PKD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5972
Polymers18,0921
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PKD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5972
Polymers18,0921
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.439, 58.119, 91.185
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 PKD domain-containing protein


Mass: 18092.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: isolated carbohydrate binding module part of the protein with Uniprot code A0M709
Source: (gene. exp.) Christiangramia forsetii KT0803 (bacteria)
Gene: GFO_3465
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0M709
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.18 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 292 K / Method: counter-diffusion / pH: 7
Details: 2.5 M ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0, 6% ethanol and 4% polyethylenglycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 gasstream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→47.42 Å / Num. obs: 23977 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.81 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1610 / CC1/2: 0.58 / Rpim(I) all: 0.59 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.42 Å / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.186
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1216 5.1 %RANDOM
Rwork0.23 ---
obs0.232 22698 99.7 %-
Displacement parametersBiso mean: 32.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 68 91 2709
Refine LS restraintsType: NCS Local / Dev ideal: 0.14 / Weight: 0.05
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.403 68 -
Rwork0.395 1610 -
obs--96.94 %

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