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- PDB-7e7r: Crystal structure of RSL mutant in complex with Ligand -

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Basic information

Entry
Database: PDB / ID: 7e7r
TitleCrystal structure of RSL mutant in complex with 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: 1.82 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: To Be Published
Title: Crystal structure of RSL mutant-R17A/R108A/R199A in complex with R3F
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
Water7,224401
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)67.427, 81.959, 97.116
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 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.: 401 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
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: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.82→62.64 Å / Num. obs: 49086 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.052 / Rrim(I) all: 0.191 / Net I/σ(I): 10.8 / Num. measured all: 647333 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.82-1.92131.4359176770390.9040.4091.4932.7
5.75-62.6411.30.0541942817180.9980.0170.05725.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CSD

4csd


Resolution: 1.82→62.64 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 2402 4.93 %RANDOM
Rwork0.2499 46352 --
obs0.2516 48754 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 26.8866 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 1.82→62.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 330 401 4641
Biso mean--62.72 26.01 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.860.35331200.332126942814100
1.86-1.90.34651360.314726842820100
1.9-1.940.30571390.299127052844100
1.94-1.990.28331360.278726922828100
1.99-2.040.30431280.274427122840100
2.04-2.10.25981530.270427032856100
2.1-2.170.35671360.255827042840100
2.17-2.250.31251310.245427052836100
2.25-2.340.31181310.252327152846100
2.34-2.450.2441540.239826822836100
2.45-2.580.27471380.250827432881100
2.58-2.740.29711480.252227042852100
2.74-2.950.29811540.248627432897100
2.95-3.240.28181400.237227412881100
3.24-3.710.25481570.225527422899100
3.71-4.680.25691480.212427922940100
4.68-62.640.28961530.25672891304498
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)
11.99430.2690.23590.37060.23161.18360.0069-0.12690.0784-0.0162-0.04740.0358-0.0501-0.06550.0310.1242-0.00040.00220.36350.00980.1282-11.1608-13.17639.4829
22.2036-0.0218-0.24320.58630.15551.49530.01990.1583-0.0699-0.0275-0.0321-0.00910.0601-0.07980.00340.10710.0024-0.0030.2805-00.117312.089213.2965-9.62
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:501)A2 - 501
2X-RAY DIFFRACTION2(chain B and resseq 1:501)B1 - 501

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