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- PDB-5t1x: Crystal Structure of Native Tarin Lectin -

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Basic information

Entry
Database: PDB / ID: 5t1x
TitleCrystal Structure of Native Tarin Lectin
Components(Lectin) x 2
KeywordsSUGAR BINDING PROTEIN / Tarin / GNA-related Lectin
Function / homology
Function and homology information


response to other organism / D-mannose binding / extracellular region
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
TRIETHYLENE GLYCOL / Mannose-specific lectin 2 / Mannose-specific lectin 1
Similarity search - Component
Biological speciesColocasia esculenta (taro)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPereira, P.R. / Meagher, J.L. / Stuckey, J.A.
Funding support Brazil, United States, 3items
OrganizationGrant numberCountry
Conselho Nacional de Desenvolvimento Cientifico e Tecnologico142475/ 2008-4 Brazil
Fulbright ProgramBEX 3421/10-4 Brazil
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor085P1000817 United States
CitationJournal: Glycobiology / Year: 2017
Title: High-resolution crystal structures of Colocasia esculenta tarin lectin.
Authors: Pereira, P.R. / Meagher, J.L. / Winter, H.C. / Goldstein, I.J. / Paschoalin, V.M. / Silva, J.T. / Stuckey, J.A.
History
DepositionAug 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Lectin
B: Lectin
C: Lectin
D: Lectin
E: Lectin
F: Lectin
G: Lectin
H: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,27617
Polymers97,4538
Non-polymers8239
Water12,881715
1
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4253
Polymers24,3632
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-27 kcal/mol
Surface area10230 Å2
MethodPISA
2
C: Lectin
D: Lectin


Theoretical massNumber of molelcules
Total (without water)24,3632
Polymers24,3632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-28 kcal/mol
Surface area9860 Å2
MethodPISA
3
E: Lectin
F: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9128
Polymers24,3632
Non-polymers5496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-27 kcal/mol
Surface area10150 Å2
MethodPISA
4
G: Lectin
H: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5754
Polymers24,3632
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-27 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.700, 82.710, 122.700
Angle α, β, γ (deg.)90.000, 91.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Lectin /


Mass: 12053.487 Da / Num. of mol.: 4 / Fragment: UNP residues 24-133 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / References: UniProt: A5HMM7
#2: Protein
Lectin /


Mass: 12309.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / References: UniProt: Q39487*PLUS

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Non-polymers , 4 types, 724 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 25-35% Peg 3350, 0.2M Lithium Sulfate, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 23, 2008 / Details: mirrors
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 104443 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 18.41 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.381 / Rejects: 0 / % possible all: 98.1

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
HKL-2000data reduction
PDB_EXTRACT3.1data extraction
HKL-2000data scaling
BUSTER2.11.1refinement
BALBESphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLP

1dlp


Resolution: 1.7→17.14 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5214 5 %RANDOM
Rwork0.18 ---
obs0.181 104362 99.8 %-
Displacement parametersBiso max: 110.18 Å2 / Biso mean: 21.01 Å2 / Biso min: 4.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.2362 Å20 Å2-0.039 Å2
2---0.2108 Å20 Å2
3---0.4471 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.7→17.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 49 715 7536
Biso mean--34.78 31.59 -
Num. residues----872
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3162SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes197HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1040HARMONIC5
X-RAY DIFFRACTIONt_it7029HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion861SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8339SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7029HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9553HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion4.17
X-RAY DIFFRACTIONt_other_torsion2.45
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 388 5.09 %
Rwork0.196 7229 -
all-7617 -
obs--99.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6090.0060.040.89810.68892.3006-0.0622-0.0368-0.07520.2567-0.04040.06250.5641-0.13970.10250.0637-0.01540.0484-0.10810.007-0.045853.7971-9.628222.3062
20.3431-0.0844-0.21570.3744-0.14120.6217-0.0325-0.0074-0.00960.01880.0033-0.00420.0198-0.01570.0292-0.0373-0.0118-0.002-0.0241-0.00430.02456.93329.198710.0648
30.97770.3048-0.21460.4659-0.2711.5801-0.0904-0.0643-0.10320.0255-0.0186-0.11560.24350.34660.1089-0.02970.08180.0141-0.00970.0303-0.046166.4509-1.659340.1328
40.49210.0122-0.42040.6369-0.2180.8637-0.04-0.0482-0.03890.04710.02770.01060.08050.01360.0123-0.0010.02820.0024-0.00330.0085-0.052548.14334.061852.1218
50.68920.1454-0.20280.5682-0.2961.90220.0382-0.06060.04930.156-0.00010.0017-0.40290.1201-0.03810.0283-0.0125-0.0145-0.0863-0.0059-0.042441.345841.667822.7031
60.27930.04710.11740.46620.14490.5535-0.0275-0.00660.01250.02160.00230.0167-0.0076-0.00730.0252-0.0403-0.0057-0.0019-0.01930.00250.026738.147222.802610.2853
70.87480.09920.0930.45390.17931.219-0.0428-0.04030.0504-0.0016-0.02740.1272-0.1733-0.26630.0702-0.03290.0522-0.0136-0.0055-0.0123-0.029928.0933.718740.1266
80.2419-0.34360.32070.74880.15410.6899-0.052-0.0859-0.00150.07710.0727-0.019-0.0562-0.001-0.0207-0.01950.0173-0.00570.00690.0037-0.049146.239327.423852.4172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 109}A1 - 109
2X-RAY DIFFRACTION2{B|1 - 110}B1 - 110
3X-RAY DIFFRACTION3{C|1 - 109}C1 - 109
4X-RAY DIFFRACTION4{D|1 - 109}D1 - 109
5X-RAY DIFFRACTION5{E|1 - 108}E1 - 108
6X-RAY DIFFRACTION6{F|1 - 110}F1 - 110
7X-RAY DIFFRACTION7{G|1 - 109}G1 - 109
8X-RAY DIFFRACTION8{H|1 - 108}H1 - 108

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