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- PDB-3zi8: Structure of the R17A mutant of the Ralstonia soleanacerum lectin... -

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Basic information

Entry
Database: PDB / ID: 3zi8
TitleStructure of the R17A mutant of the Ralstonia soleanacerum lectin at 1.5 Angstrom in complex with L-fucose
ComponentsPUTATIVE FUCOSE-BINDING LECTIN PROTEIN
KeywordsSUGAR BINDING PROTEIN / MULTIVALENCY
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-L-fucopyranose / Putative fucose-binding lectin protein
Similarity search - Component
Biological speciesRALSTONIA SOLANACEARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsArnaud, J. / Audfray, A. / Claudinon, J. / Trondle, K. / Trosvalet, M. / Thomas, A. / Varrot, A. / Romer, W. / Imberty, A.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Reduction of Lectin Valency Drastically Changes Glycolipid Dynamics in Membranes, But not Surface Avidity.
Authors: Arnaud, J. / Claudinon, J. / Trondle, K. / Trovaslet, M. / Larson, G. / Thomas, A. / Varrot, A. / Romer, W. / Imberty, A. / Audfray, A.
History
DepositionJan 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Structure summary / Category: audit_author / diffrn_detector / Item: _audit_author.name / _diffrn_detector.type
Revision 2.0Nov 29, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_unobs_or_zero_occ_atoms / struct
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _struct.title
Revision 2.1Jul 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 / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 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
Item: _chem_comp.pdbx_synonyms / _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: PUTATIVE FUCOSE-BINDING LECTIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9544
Polymers9,6471
Non-polymers3073
Water1,892105
1
A: PUTATIVE FUCOSE-BINDING LECTIN PROTEIN
hetero molecules

A: PUTATIVE FUCOSE-BINDING LECTIN PROTEIN
hetero molecules

A: PUTATIVE FUCOSE-BINDING LECTIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,86212
Polymers28,9423
Non-polymers9209
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area7010 Å2
ΔGint-29.1 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.399, 72.399, 35.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

21A-2015-

HOH

31A-2030-

HOH

41A-2043-

HOH

51A-2063-

HOH

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Components

#1: Protein PUTATIVE FUCOSE-BINDING LECTIN PROTEIN / LECTIN


Mass: 9647.446 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: D8NA05
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST METHIONINE CLEAVED. THE NUMBERING IS ACCORDING TO THE MATURE PROTEIN AND IS SHIFTED BY ONE ...FIRST METHIONINE CLEAVED. THE NUMBERING IS ACCORDING TO THE MATURE PROTEIN AND IS SHIFTED BY ONE COMPARED TO THE DEPOSITED ONE

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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: 2.8 Å3/Da / Density % sol: 56.2 % / Description: NONE
Crystal growpH: 6.5
Details: 30MM MGCL2, 30MM CACL2, 100MM MES/IMIDAZOLE PH 6.5, 12.5 % OF MPD, PEG1K AND PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→36.2 Å / Num. obs: 17523 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.8 / % possible all: 98.7

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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: 1.5→36.2 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.97 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED SIDE CHAIN WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1656 892 5.1 %RANDOM
Rwork0.13357 ---
obs0.1351 16628 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.33 Å20 Å2
2--0.33 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 19 105 806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02761
X-RAY DIFFRACTIONr_bond_other_d0.0010.02660
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.8971054
X-RAY DIFFRACTIONr_angle_other_deg0.84631516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.849598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77424.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8481596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.892152
X-RAY DIFFRACTIONr_chiral_restr0.1140.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
X-RAY DIFFRACTIONr_nbd_refined0.2410.2188
X-RAY DIFFRACTIONr_nbd_other0.1980.2550
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2343
X-RAY DIFFRACTIONr_nbtor_other0.0930.2395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1981.696380
X-RAY DIFFRACTIONr_mcbond_other2.161.688379
X-RAY DIFFRACTIONr_mcangle_it2.4772.545476
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.221.9381
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.53331421
X-RAY DIFFRACTIONr_sphericity_free19.038543
X-RAY DIFFRACTIONr_sphericity_bonded6.4851460
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 65 -
Rwork0.125 1215 -
obs--99.61 %

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