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- PDB-2jdz: Crystal structure of recombinant Dioclea guianensis lectin comple... -

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Basic information

Entry
Database: PDB / ID: 2jdz
TitleCrystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose
ComponentsLECTIN ALPHA CHAIN
KeywordsCARBOHYDRATE-BINDING PROTEIN / METAL-BINDING / LEGUME LECTIN
Function / homology
Function and homology information


D-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 ...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: 2.1 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 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 29, 2012Group: Database references / Other
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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 1.5Dec 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

Downloads & links

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Assembly

Deposited unit
A: LECTIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4899
Polymers25,6531
Non-polymers8368
Water1,44180
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)105,95736
Polymers102,6134
Non-polymers3,34332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area8550 Å2
ΔGint-62.4 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.222, 89.222, 106.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein LECTIN ALPHA CHAIN / RDGUIA


Mass: 25653.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DIOCLEA GUIANENSIS (plant) / Plasmid: RDGUIA/PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81637
#5: 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

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Non-polymers , 4 types, 87 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / 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: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AMINO ACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS WITH THE AMINO ACID SEQUENCE ...THE AMINO ACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS WITH THE AMINO ACID 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.

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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: 2.1 Å3/Da / Density % sol: 40.1 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 30% PEG 400, 0.1M MES, PH 6.5 AND 0.1M CDCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9308
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9308 Å / Relative weight: 1
ReflectionResolution: 2.1→34.1 Å / Num. obs: 12834 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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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 1H9P

1h9p


Resolution: 2.1→34.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.673 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 971 7.6 %RANDOM
Rwork0.196 ---
obs0.2 11848 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 30 80 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9642495
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.195232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40924.44472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61915270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.511157
X-RAY DIFFRACTIONr_chiral_restr0.1120.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2815
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21291
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4050.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8331.51181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45221883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2713741
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4834.5612
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: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 75 -
Rwork0.205 854 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.1149 Å / Origin y: 2.0047 Å / Origin z: 14.2788 Å
111213212223313233
T-0.1316 Å2-0.0232 Å2-0.0593 Å2--0.025 Å20.1177 Å2---0.0788 Å2
L2.2726 °20.2984 °20.0768 °2-1.8375 °2-0.6653 °2--1.9645 °2
S0.1263 Å °-0.1638 Å °-0.1089 Å °0.1464 Å °-0.375 Å °-0.3011 Å °-0.0839 Å °0.1979 Å °0.2487 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 239
2X-RAY DIFFRACTION1A240 - 248
3X-RAY DIFFRACTION1A249
4X-RAY DIFFRACTION1A2001 - 2080

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