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- PDB-4csd: Structure of Monomeric Ralstonia solanacearum lectin -

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Basic information

Entry
Database: PDB / ID: 4csd
TitleStructure of Monomeric Ralstonia solanacearum lectin
ComponentsFUCOSE-BINDING LECTIN PROTEIN
KeywordsFUCOSE-BINDING PROTEIN / BETA PROPELLER
Function / homologyFucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta / methyl alpha-L-fucopyranoside / Fucose-binding lectin protein
Function and homology information
Biological speciesRALSTONIA SOLANACEARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsArnaud, J. / Trundle, K. / Claudinon, J. / Audfray, A. / Varrot, A. / Romer, W. / Imberty, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Membrane Deformation by Neolectins with Engineered Glycolipid Binding Sites.
Authors: Arnaud, J. / Trondle, K. / Claudinon, J. / Audfray, A. / Varrot, A. / Romer, W. / Imberty, A.
History
DepositionMar 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Other
Revision 1.2Sep 13, 2017Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.type / _struct.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FUCOSE-BINDING LECTIN PROTEIN
B: FUCOSE-BINDING LECTIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,93015
Polymers58,7002
Non-polymers2,23013
Water11,764653
1
A: FUCOSE-BINDING LECTIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5118
Polymers29,3501
Non-polymers1,1617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FUCOSE-BINDING LECTIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4197
Polymers29,3501
Non-polymers1,0696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.420, 75.910, 85.780
Angle α, β, γ (deg.)90.00, 102.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 270 / Label seq-ID: 2 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.9999, 0.001556, -0.01016), (0.009663, 0.4795, -0.8775), (0.003506, -0.8776, -0.4795)
Vector: -22.67, 18.94, 72.37)

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Components

#1: Protein FUCOSE-BINDING LECTIN PROTEIN / LECTIN FROM RALSTONIA SOLANACEARUM


Mass: 29349.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MONOMERIC CHIMERA OF THE WILD TYPE RSL / Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Plasmid: PET-TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q8XXK6
#2: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACIDS 0 TO 88 OF MONOMERIC RSL CORRESPOND TO AMINO ACIDS 1 TO 89 OF RSL. AMINO ACIDS 95 TO ...AMINO ACIDS 0 TO 88 OF MONOMERIC RSL CORRESPOND TO AMINO ACIDS 1 TO 89 OF RSL. AMINO ACIDS 95 TO 179 OF MONOMERIC RSL CORRESPOND TO AMINO ACIDS 5 TO 89 OF RSL. AMINO ACIDS 186 TO 271 OF MONOMERIC RSL CORRESPOND TO AMINO ACIDS 5 TO 90 OF RSL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.22 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS HYDROCHLORIDE PH 8.5, 2M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.35→41.92 Å / Num. obs: 99018 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.6 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BT9

2bt9


Resolution: 1.35→41.92 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.324 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14875 4951 5 %RANDOM
Rwork0.11555 ---
obs0.11721 94040 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.35→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 150 653 4876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024367
X-RAY DIFFRACTIONr_bond_other_d0.0070.023741
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9076004
X-RAY DIFFRACTIONr_angle_other_deg2.50438603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4445530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73923.41173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1315553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.3851518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024886
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021064
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0031.2022132
X-RAY DIFFRACTIONr_mcbond_other1.9771.2012131
X-RAY DIFFRACTIONr_mcangle_it2.3351.8062658
X-RAY DIFFRACTIONr_mcangle_other2.3451.8072659
X-RAY DIFFRACTIONr_scbond_it1.9051.2412235
X-RAY DIFFRACTIONr_scbond_other1.9041.2412235
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2681.8073347
X-RAY DIFFRACTIONr_long_range_B_refined3.80111.335488
X-RAY DIFFRACTIONr_long_range_B_other3.11410.4665146
X-RAY DIFFRACTIONr_rigid_bond_restr7.78338108
X-RAY DIFFRACTIONr_sphericity_free26.2335173
X-RAY DIFFRACTIONr_sphericity_bonded7.56858459
Refine LS restraints NCS

Ens-ID: 1 / Number: 13820 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 332 -
Rwork0.137 6402 -
obs--91.87 %

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