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- PDB-7e7n: Crystal structure of RSL mutant-R17A/R108A/R199A in complex with R3F -

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Basic information

Entry
Database: PDB / ID: 7e7n
TitleCrystal structure of RSL mutant-R17A/R108A/R199A in complex with R3F
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-R3F / Fucose-binding lectin protein / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: To Be Published
Title: Crystal structure of RSL mutant in complex with suger Ligand
Authors: Li, L. / Chen, G.S.
History
DepositionFeb 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7807
Polymers29,0921
Non-polymers2,6886
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.300, 45.635, 46.844
Angle α, β, γ (deg.)94.120, 117.040, 117.200
Int Tables number1
Space group name H-MP1

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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.: 1 / 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, UniProt: A0A0S4WQH1*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-R3F / 2-[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]ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 803.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H57N5O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
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 buffer, the ligand solution

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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: Jun 21, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.5→39.04 Å / Num. obs: 40510 / % possible obs: 93.8 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.027 / Rrim(I) all: 0.051 / Net I/σ(I): 14.2 / Num. measured all: 143079 / Scaling rejects: 46
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
1.5-1.593.60.482113859140.8820.2960.5652.693.6
4.76-39.043.50.026450112920.9980.0160.03137.294.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CSD

4csd


Resolution: 1.55→39.04 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.871 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 2049 5.7 %RANDOM
Rwork0.1715 ---
obs0.1731 33948 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.9 Å2 / Biso mean: 19.97 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å20 Å2
2--0 Å20.01 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.55→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 192 150 2311
Biso mean--70.03 23.8 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181867
X-RAY DIFFRACTIONr_angle_refined_deg2.2271.7533070
X-RAY DIFFRACTIONr_angle_other_deg1.7351.6974313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6895256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0522.92189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.825156
X-RAY DIFFRACTIONr_chiral_restr0.7580.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 118 -
Rwork0.201 2120 -
all-2238 -
obs--75.99 %
Refinement TLS params.Method: refined / Origin x: 2.069 Å / Origin y: 8.765 Å / Origin z: 4.946 Å
111213212223313233
T0.0076 Å20.01 Å2-0.0014 Å2-0.016 Å20.0033 Å2--0.0161 Å2
L0.3031 °20.3755 °2-0.1549 °2-0.6625 °20.1742 °2--0.7595 °2
S0.013 Å °0.0041 Å °0.0033 Å °0.0123 Å °0.003 Å °-0.0014 Å °-0.0142 Å °-0.0033 Å °-0.016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 269
2X-RAY DIFFRACTION1A401 - 406

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