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- PDB-7e7w: Crystal structure of RSL mutant in complex with sugar Ligand -

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Basic information

Entry
Database: PDB / ID: 7e7w
TitleCrystal structure of RSL mutant in complex with sugar Ligand
ComponentsFucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Complex / Lectin / Fucose / Rhodamine
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: To Be Published
Title: Crystal structure of RSL mutant in complex with sugar Ligand
Authors: Li, L. / Chen, G.S.
History
DepositionFeb 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)88,0503
Polymers88,0503
Non-polymers00
Water00
1
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.567, 46.554, 103.254
Angle α, β, γ (deg.)90.040, 89.920, 119.980
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 29349.916 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: 20 mM Tris-HCl, 100 mM of NaCl pH 7.5, the crystal was obtained in Micro centrifuge tube sequentially put with RSL solution, pure buffer, and the ligand solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 4.1→30 Å / Num. obs: 6095 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.078 / Rrim(I) all: 0.143 / Χ2: 0.718 / Net I/σ(I): 4.7 / Num. measured all: 19061
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.1-4.2530.46290.8690.2630.480.84398.9
4.25-4.4230.2816060.9210.1860.3380.88799.2
4.42-4.623.10.1976050.970.1270.2350.9299
4.62-4.863.20.2226030.9410.140.2630.8599.2
4.86-5.1630.1256200.9850.0840.1510.7899
5.16-5.562.90.145810.9580.0950.1710.70899.7
5.56-6.113.20.146260.9630.0910.1680.65799.7
6.11-6.993.40.1076110.9850.0660.1260.63898.7
6.99-8.773.30.0635960.9930.0390.0740.45799.2
8.77-303.10.0386180.990.0250.0450.47899.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CSD

4csd


Resolution: 4.1→26.2 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3467 245 4.24 %RANDOM
Rwork0.2004 5530 --
obs0.2063 5775 98.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.52 Å2 / Biso mean: 82.1568 Å2 / Biso min: 31.08 Å2
Refinement stepCycle: final / Resolution: 4.1→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 0 0 6063
Num. residues----792
LS refinement shellResolution: 4.101→4.247 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.36 18 -
Rwork0.1588 622 -
obs--99 %

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