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- PDB-7e7t: Crystal structure of RSL mutant in complex with sugar Ligand -

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Basic information

Entry
Database: PDB / ID: 7e7t
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 / Chem-R2F / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: To Be Published
Title: Crystal structure of RSL mutant-R17A/R108A/R199A in complex with R2F
Authors: Li, L. / Chen, G.S.
History
DepositionFeb 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7428
Polymers58,1832
Non-polymers4,5596
Water1,60389
1
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3714
Polymers29,0921
Non-polymers2,2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3714
Polymers29,0921
Non-polymers2,2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.342, 88.554, 67.893
Angle α, β, γ (deg.)90.000, 93.830, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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: 29091.568 Da / Num. of mol.: 2 / Mutation: R17A,R108A,R199A
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
#2: Chemical
ChemComp-R2F / 2-[2-[4-[[(2R,3S,4R,5S,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-1,2,3-triazol-1-yl]ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 759.888 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H53N5O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: 20 mM Tris-HCl, 100 mM of NaCl; pH 7.5, Micro centrifuge tube sequentially put with RSL solution, pure b

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.98→67.74 Å / Num. obs: 32990 / % possible obs: 89.6 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 9.2 / Num. measured all: 210690
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.98-2.086.50.5482584239780.9280.230.5953.174.5
6.25-67.7460.066718512020.9960.0280.07217.399.5

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Processing

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

4csd


Resolution: 1.98→67.74 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1615 4.98 %RANDOM
Rwork0.257 30786 --
obs0.2593 32401 88.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.98 Å2 / Biso mean: 39.9042 Å2 / Biso min: 18.57 Å2
Refinement stepCycle: final / Resolution: 1.98→67.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 330 89 4363
Biso mean--84.17 30.86 -
Num. residues----519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.040.33391480.311328492997100
2.04-2.10.3687680.3391349141746
2.1-2.180.36231510.308428242975100
2.18-2.230.4041940.30271763185797
2.27-2.370.39031460.31542811295797
2.37-2.490.36121600.29462825298599
2.49-2.650.36421240.32882300699
2.71-2.860.3624880.31371955204397
2.86-3.140.37551370.28272874301199
3.14-3.60.27861600.247428903050100
3.6-4.530.25581790.218428683047100
4.53-67.740.24541600.20672896305699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.85620.3984-0.32521.6528-0.26743.0171-0.0526-0.00120.0349-0.22040.10730.10290.2006-0.2592-0.03240.32450.0063-0.05570.22070.00320.186413.4566.296-0.248
21.16910.4482-0.06721.34610.64772.6485-0.0173-0.0284-0.0588-0.15790.0839-0.0918-0.20010.195-0.06450.37790.0099-0.05770.21-0.00630.205933.22522.722-32.963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:269 OR RESID 301:303 ) )A1 - 269
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:269 OR RESID 301:303 ) )A301 - 303
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:269 OR RESID 301:303 ) )B1 - 269
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:269 OR RESID 301:303 ) )B301 - 303

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