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- PDB-2je7: Crystal structure of recombinant Dioclea guianensis lectin S131H ... -

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Basic information

Entry
Database: PDB / ID: 2je7
TitleCrystal structure of recombinant Dioclea guianensis lectin S131H complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose
ComponentsLECTIN ALPHA CHAIN
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING PROTEIN / CONA-LIKE / METAL-BINDING / LEGUME LECTIN / RECOMBINANT LECTIN / SUGAR-BINDING PROTEIN
Function / homology
Function and homology information


mannose binding / toxin activity / carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-XMM / Lectin alpha chain
Similarity search - Component
Biological speciesDIOCLEA GUIANENSIS (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNagano, C.S. / Sanz, L. / Cavada, B.S. / Calvete, J.J.
CitationJournal: Biochem.J. / Year: 2008
Title: Insights Into the Structural Basis of the Ph- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins.
Authors: Nagano, C.S. / Calvete, J.J. / Barettino, D. / Perez, A. / Cavada, B.S. / Sanz, L.
History
DepositionJan 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LECTIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2084
Polymers25,7041
Non-polymers5043
Water4,594255
1
A: LECTIN ALPHA CHAIN
hetero molecules

A: LECTIN ALPHA CHAIN
hetero molecules

A: LECTIN ALPHA CHAIN
hetero molecules

A: LECTIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,83216
Polymers102,8184
Non-polymers2,01512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11170 Å2
ΔGint-148.5 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.661, 88.014, 91.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein LECTIN ALPHA CHAIN / RDGUIA


Mass: 25704.430 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DIOCLEA GUIANENSIS (plant) / Plasmid: RDGUIAS131H/PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81637
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 131 TO HIS
Sequence detailsTHE AMINOACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS WITH THE AMINOACID SEQUENCE DETERMINED ...THE AMINOACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS WITH THE AMINOACID SEQUENCE DETERMINED BY DIRECT METHOD. THE DEDUCED SEQUENCE WAS CONFIRMED BY SEQUENCE OF ALL CLONES (FROM CDNA AND GENOMIC DNA). THE INSERTIONS AT N-TERMINAL ARE DUE THE NCOI RESTRICTION SITE OF THE PET-32A VECTOR. THE SEQUENCE FROM 2JDZ WAS USED AS TEMPLATE FOR SITE DIRECTED MUTAGENESIS OF RESIDUE 133.

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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: 2.6 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growpH: 7
Details: CRYSTALS WERE GROWN WITH 0.6M NACL, 0.1 HEPES, PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→44 Å / Num. obs: 31757 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H9W

1h9w


Resolution: 1.65→63.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.462 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1614 5.1 %RANDOM
Rwork0.154 ---
obs0.156 30142 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.65→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 25 255 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9632664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10624.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69115303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.353159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021472
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2932
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21390
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2461.51242
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96321994
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9423798
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9594.5659
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 125
Rwork0.204 2237
Refinement TLS params.Method: refined / Origin x: 18.5263 Å / Origin y: 29.7654 Å / Origin z: 10.4425 Å
111213212223313233
T-0.0004 Å2-0.0083 Å20.0065 Å2--0.0103 Å20.0026 Å2---0.0257 Å2
L0.1489 °20.0085 °2-0.1072 °2-0.4302 °2-0.0582 °2--0.3657 °2
S0.0152 Å °-0.0026 Å °-0.0224 Å °0.0286 Å °-0.0043 Å °0.0539 Å °-0.0166 Å °0.0076 Å °-0.0109 Å °

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