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- PDB-7e7v: Crystal structure of RSL mutant in complex with sugar Ligand -

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Basic information

Entry
Database: PDB / ID: 7e7v
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-R3F / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: To Be Published
Title: Crystal structure of RSL mutant in complex with 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,94521
Polymers87,0163
Non-polymers5,92918
Water8,503472
1
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9827
Polymers29,0051
Non-polymers1,9766
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)30,9827
Polymers29,0051
Non-polymers1,9766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9827
Polymers29,0051
Non-polymers1,9766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.494, 161.519, 54.137
Angle α, β, γ (deg.)90.000, 91.530, 90.000
Int Tables number4
Space group name H-MP1211

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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: 29005.451 Da / Num. of mol.: 3 / Mutation: R17A,R108A,R153A,R244A
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-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.: 6 / Source method: obtained synthetically / Formula: C43H57N5O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
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, 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: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.61→80.76 Å / Num. obs: 94580 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 15 / Num. measured all: 597512 / Scaling rejects: 1268
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
1.61-1.694.80.5964788135520.8320.2960.6622.796.7
5.08-80.766.80.0572104331160.9980.0240.0623299.8

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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: 1.61→80.76 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.765 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 4739 5 %RANDOM
Rwork0.2178 ---
obs0.2194 89341 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.92 Å2 / Biso mean: 21.416 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.09 Å2
2--0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.61→80.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 0 420 472 6979
Biso mean--55.18 25.31 -
Num. residues----808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136721
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185612
X-RAY DIFFRACTIONr_angle_refined_deg1.961.7149235
X-RAY DIFFRACTIONr_angle_other_deg1.5851.65312984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2775801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15123.218261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5431515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021510
LS refinement shellResolution: 1.61→1.65 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.301 302 -
Rwork0.288 6371 -
obs--94.41 %
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)
10.51650.27590.11910.5740.22220.7408-0.08360.00970.03860.020.0576-0.02630.00350.07160.0260.02930.0089-0.00380.0479-0.01390.03237.9635-14.752466.1524
20.2132-0.2742-0.05060.70590.10631.0977-0.0449-0.0054-0.0891-0.0458-0.07030.1405-0.0122-0.05760.11520.040.01670.01440.049-0.02820.0611-10.3976-40.673439.4003
30.38740.2462-0.14571.4571-0.62711.0976-0.12620.01980.0027-0.0180.1240.182-0.007-0.00320.00220.0472-0.0041-0.00340.01430.02490.0635-10.709411.279639.6024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 401
2X-RAY DIFFRACTION2B1 - 401
3X-RAY DIFFRACTION3C2 - 401

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