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- PDB-5d5g: Structure of colocasia esculenta agglutinin -

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Basic information

Entry
Database: PDB / ID: 5d5g
TitleStructure of colocasia esculenta agglutinin
Components(Tuber agglutinin) x 2
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING / LECTIN / AGGLUTININ / BETA PRISM II
Function / homology
Function and homology information


response to other organism / D-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
Mannose-specific lectin CEA
Similarity search - Component
Biological speciesColocasia esculenta (taro)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsBiswas, H. / Chattopadhyaya, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technologynone India
Citation
Journal: J GLYCOBIO / Year: 2017
Title: Crystal structure Colocasia esculenta tuber agglutinin at 1.74A resolution and its quaternary interactions
Authors: Chattopadhyaya, R. / Biswas, H. / Sarkar, A.
#1: Journal: J. Biomol. Struct. Dyn. / Year: 2017
Title: Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from alpha 2 beta 2 to unfolded state
Authors: Biswas, H. / Chattopadhyaya, R.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.journal_id_ISSN
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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
C: Tuber agglutinin
D: Tuber agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,31811
Polymers48,8634
Non-polymers4567
Water2,414134
1
A: Tuber agglutinin
B: Tuber agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8879
Polymers24,4312
Non-polymers4567
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-50 kcal/mol
Surface area10350 Å2
MethodPISA
2
C: Tuber agglutinin
D: Tuber agglutinin


Theoretical massNumber of molelcules
Total (without water)24,4312
Polymers24,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-25 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.012, 47.198, 82.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Tuber agglutinin


Mass: 12012.415 Da / Num. of mol.: 2 / 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: 12418.863 Da / Num. of mol.: 2 / Fragment: UNP residues 140-250 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / Plasmid details: local market, food item / Tissue: tuber / References: UniProt: R9RL27

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Non-polymers , 4 types, 141 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.42 Å3/Da / Density % sol: 49.27 % / Description: rectangular plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: reservoir included 1.8 M ammonium sulphate and 0.1 M Hepes, pH 6.0; stock protein solution contained 8.1 mg/ml of lectin in 20 mM Tris pH 8.5; protein & reservoir soln mixed in 3:1 ratio at ...Details: reservoir included 1.8 M ammonium sulphate and 0.1 M Hepes, pH 6.0; stock protein solution contained 8.1 mg/ml of lectin in 20 mM Tris pH 8.5; protein & reservoir soln mixed in 3:1 ratio at start and placed on siliconized cover slip
Temp details: fluctuated within 5 K

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Data collection

DiffractionMean temperature: 113 K / Ambient temp details: over 2 days, 8 min per frame
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 5, 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: 1.536→21 Å / Num. obs: 59836 / % possible obs: 83.4 % / Redundancy: 5.61 % / Rmerge(I) obs: 0.38 / Rsym value: 0.38 / Net I/σ(I): 2.7
Reflection shellResolution: 1.536→1.58 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 0.9 / % possible all: 20

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0E

3r0e


Resolution: 1.74→20.986 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 60.71 / Stereochemistry target values: ML
Details: THERE ARE 7 PROTEIN ATOMS AND 5 WATER MOLECULARS WITH ZERO B FACTORS. AUTHOR HAS CONFIRMED THESE ATOMS AND STATED: 7 PROTEIN ATOMS WITH ZERO B FACTORS AFTER PHENIX REFINEMENT, FOUND TO ...Details: THERE ARE 7 PROTEIN ATOMS AND 5 WATER MOLECULARS WITH ZERO B FACTORS. AUTHOR HAS CONFIRMED THESE ATOMS AND STATED: 7 PROTEIN ATOMS WITH ZERO B FACTORS AFTER PHENIX REFINEMENT, FOUND TO POSSESS QUITE STRONG ELECTRON DENSITIES. THE 5 WATER MOLECULES WITH ZERO TEMPERATURE FACTORS COULD VERY WELL BE SODIUM CATIONS WHICH ARE ISO-ELECTRONIC WITH WATER OXYGEN ATOMS. HOWEVER NA+ IONS SHOULD HAVE HIGHER ELECTRON DENSITIES AT THEIR CENTERS COMPARED TO OXYGEN, DUE TO A HIGHER ATOMIC NUMBER.
RfactorNum. reflection% reflection
Rfree0.4272 837 1.7 %
Rwork0.3441 48357 -
obs0.3455 49194 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.33 Å2 / Biso mean: 19.0229 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.74→20.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 25 134 3577
Biso mean--22.24 15.01 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083523
X-RAY DIFFRACTIONf_angle_d1.3764774
X-RAY DIFFRACTIONf_chiral_restr0.084504
X-RAY DIFFRACTIONf_plane_restr0.005620
X-RAY DIFFRACTIONf_dihedral_angle_d14.7631247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.8490.39561250.38527648777396
1.849-1.99160.44361500.399280228172100
1.9916-2.19190.4261230.402480588181100
2.1919-2.50860.44211420.375380828224100
2.5086-3.15880.42621530.374581418294100
3.1588-20.98760.42651440.279384068550100

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