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- PDB-7dc0: Crystal structure of glycan-free Pseudomonas taiwanensis lectin -

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Basic information

Entry
Database: PDB / ID: 7dc0
TitleCrystal structure of glycan-free Pseudomonas taiwanensis lectin
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / beta barrel / antiviral lectin / carbohydrate binding
Biological speciesPseudomonas taiwanensis DSM 21245 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsOda, K. / Matoba, Y.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity.
Authors: Matoba, Y. / Sato, Y. / Oda, K. / Hatori, Y. / Morimoto, K.
History
DepositionOct 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9707
Polymers28,4892
Non-polymers4805
Water4,306239
1
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5334
Polymers14,2451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6640 Å2
MethodPISA
2
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4373
Polymers14,2451
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area6670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.129, 44.151, 134.818
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 Lectin


Mass: 14244.618 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas taiwanensis DSM 21245 (bacteria)
Gene: PTL / Plasmid: pET101/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.64 % / Mosaicity: 0.47 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulfate, Mes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 22280 / Num. obs: 22280 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.076 / Rrim(I) all: 0.186 / Rsym value: 0.161 / Net I/σ(I): 8.9 / Num. measured all: 127644
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.88-1.9860.5551930832030.8850.0250.0580.0514.3100
5.95-505.30.05143588180.9970.0270.0630.05314.399.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s5v

3s5v


Resolution: 1.88→19.81 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1159 5.22 %
Rwork0.1786 21031 -
obs0.1806 22190 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.59 Å2 / Biso mean: 12.9118 Å2 / Biso min: 1.2 Å2
Refinement stepCycle: final / Resolution: 1.88→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 25 241 2280
Biso mean--42.7 22.84 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.88-1.970.25191420.202225852727
1.97-2.070.2141310.176825892720
2.07-2.20.24191300.17926212751
2.2-2.370.23391760.184325462722
2.37-2.610.20631210.190826572778
2.61-2.980.23541460.179126102756
2.98-3.750.18281460.156926492795
3.76-19.810.20941670.180927742941

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