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- PDB-5d9z: Structure of Colocasia Esculenta Agglutinin with mannose bound -

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Basic information

Entry
Database: PDB / ID: 5d9z
TitleStructure of Colocasia Esculenta Agglutinin with mannose bound
Components(Tuber agglutinin) x 2
KeywordsSUGAR BINDING PROTEIN / LECTIN / PROTEIN-CARBOHYDRATE INTERACTIONS / DIETARY PROTEIN / BETA PRISM II FOLD / 18-AUG
Function / homology
Function and homology information


response to other organism / mannose binding / extracellular region / metal ion binding
Similarity search - Function
Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / PHOSPHATE ION / Mannose-specific lectin CEA
Similarity search - Component
Biological speciesColocasia esculenta (taro)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChattopadhyaya, R.
Funding support India, 1items
OrganizationGrant numberCountry
DST, Government of IndiaInstitutional India
CitationJournal: to be published
Title: High resolution crystal structures of Colocasia esculenta agglutinin with and without mannose
Authors: Chattopadhyaya, R.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Tuber agglutinin
B: Tuber agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4988
Polymers24,5022
Non-polymers9966
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-32 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.896, 75.896, 124.065
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-319-

HOH

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Components

#1: Protein Tuber agglutinin


Mass: 12012.415 Da / Num. of mol.: 1 / Fragment: UNP residues 24-132 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / Plasmid details: local market, food item / Tissue: tuber / References: UniProt: R9RL27
#2: Protein Tuber agglutinin


Mass: 12489.940 Da / Num. of mol.: 1 / Fragment: UNP residues 140-251 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / Plasmid details: local market, food item / Tissue: tuber / References: UniProt: R9RL27
#3: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 4.23 Å3/Da / Density % sol: 70.89 % / Description: resembles a piece of cut diamond
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50 molar excess of D-Mannose was added to the purified 8.10 mg/ml lectin stock solution; 2 vols of this was mixed with 1 vol of crystallizing agent containing 0.1 M sodium citrate tribasic ...Details: 50 molar excess of D-Mannose was added to the purified 8.10 mg/ml lectin stock solution; 2 vols of this was mixed with 1 vol of crystallizing agent containing 0.1 M sodium citrate tribasic pH 5.6 and 1.0 M ammonium phosphate monobasic; equilibrated with above crystallizing agent in reservoir; large crystals in 3 weeks
Temp details: fluctuated within 5K

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2014
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.7→29.04 Å / Num. obs: 39501 / % possible obs: 85.6 % / Redundancy: 9.13 % / Rmerge(I) obs: 0.313 / Net I/σ(I): 4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.3 / % possible all: 24.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0E

3r0e


Resolution: 1.85→19.803 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 60.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3693 698 1.98 %Random selection
Rwork0.3156 ---
obs0.3166 35187 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 65 33 1814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111823
X-RAY DIFFRACTIONf_angle_d1.5362474
X-RAY DIFFRACTIONf_dihedral_angle_d14.922654
X-RAY DIFFRACTIONf_chiral_restr0.085278
X-RAY DIFFRACTIONf_plane_restr0.005311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.8501-1.99290.397412520.4133627890
1.9929-2.19320.46881490.43086909100
2.1932-2.510.45841290.41977022100
2.51-3.16030.38921430.36617058100
3.1603-19.80370.30771520.2251722299

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