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- PDB-7dc4: Crystal structure of glycan-bound Pseudomonas taiwanensis lectin -

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Basic information

Entry
Database: PDB / ID: 7dc4
TitleCrystal structure of glycan-bound 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 / molecular replacement / Resolution: 0.95 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

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,18810
Polymers28,4892
Non-polymers3,6998
Water9,386521
1
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9984
Polymers14,2451
Non-polymers1,7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6760 Å2
MethodPISA
2
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1906
Polymers14,2451
Non-polymers1,9465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.057, 57.862, 58.899
Angle α, β, γ (deg.)90.000, 96.950, 90.000
Int Tables number4
Space group name H-MP1211

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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: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2/a3-b1_a6-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.56 Å3/Da / Density % sol: 51.89 % / Mosaicity: 0.07 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG MME 5000, Ammonium sulfate, Mes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.85 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.95→42.74 Å / Num. obs: 180042 / % possible obs: 100 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.1 / Num. measured all: 599075 / Scaling rejects: 4957
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
0.95-0.973.20.4992834088180.7522.299.9
5.2-42.742.60.046298911530.95921.499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DC0

7dc0


Resolution: 0.95→34.38 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1477 9166 5.09 %
Rwork0.1357 170789 -
obs0.1363 179955 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.87 Å2 / Biso mean: 13.42 Å2 / Biso min: 4.45 Å2
Refinement stepCycle: final / Resolution: 0.95→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 244 526 2784
Biso mean--15.86 28.07 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
0.95-0.960.20773030.196356395942
0.96-0.970.22232710.187656845955
0.97-0.980.19882970.184857015998
0.98-10.19023070.170156635970
1-1.010.17833060.158956645970
1.01-1.020.16722760.148957085984
1.02-1.040.15243200.140556405960
1.04-1.050.13753030.135457006003
1.05-1.070.14543230.126256826005
1.07-1.090.14282970.121256585955
1.09-1.110.11823090.115656895998
1.11-1.130.12542920.107356635955
1.13-1.150.1142780.105457256003
1.15-1.170.12652920.108356635955
1.17-1.20.122940.109557516045
1.2-1.220.12232770.115857065983
1.22-1.260.12182910.115856845975
1.26-1.290.11952720.118257326004
1.29-1.330.14022970.123756745971
1.33-1.370.12743100.125856785988
1.37-1.420.12692800.120957336013
1.42-1.480.1253250.117456866011
1.48-1.540.11963400.120456435983
1.54-1.620.14333400.125856716011
1.62-1.730.14343520.130756976049
1.73-1.860.15993570.141256425999
1.86-2.050.14833200.137357086028
2.05-2.340.15773350.144357066041
2.34-2.950.17063430.159657176060
2.95-34.380.15732590.143958826141

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