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- PDB-5t20: Crystal Structure of Tarin Lectin bound to Trimannose -

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Basic information

Entry
Database: PDB / ID: 5t20
TitleCrystal Structure of Tarin Lectin bound to Trimannose
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
6alpha-alpha-mannobiose / alpha-D-mannopyranose / Mannose-specific lectin 2 / Mannose-specific lectin 1
Similarity search - Component
Biological speciesColocasia esculenta (taro)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPereira, P.R. / Meagher, J.L. / Stuckey, J.A.
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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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: Lectin
B: Lectin
C: Lectin
D: Lectin
E: Lectin
F: Lectin
G: Lectin
H: Lectin
I: Lectin
J: Lectin
K: Lectin
L: Lectin
M: Lectin
N: Lectin
O: Lectin
P: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,11935
Polymers194,90616
Non-polymers8,21319
Water15,025834
1
C: Lectin
D: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3724
Polymers24,3632
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-29 kcal/mol
Surface area10010 Å2
MethodPISA
2
E: Lectin
F: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3905
Polymers24,3632
Non-polymers1,0273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-29 kcal/mol
Surface area10110 Å2
MethodPISA
3
G: Lectin
H: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3724
Polymers24,3632
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-29 kcal/mol
Surface area10080 Å2
MethodPISA
4
I: Lectin
J: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3724
Polymers24,3632
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-28 kcal/mol
Surface area10050 Å2
MethodPISA
5
K: Lectin
L: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4345
Polymers24,3632
Non-polymers1,0713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-28 kcal/mol
Surface area9980 Å2
MethodPISA
6
M: Lectin
N: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3724
Polymers24,3632
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-28 kcal/mol
Surface area9970 Å2
MethodPISA
7
O: Lectin
P: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4345
Polymers24,3632
Non-polymers1,0713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-29 kcal/mol
Surface area9970 Å2
MethodPISA
8
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3724
Polymers24,3632
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-28 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.280, 78.828, 92.935
Angle α, β, γ (deg.)76.190, 70.440, 59.800
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Protein
Lectin


Mass: 12053.487 Da / Num. of mol.: 8 / 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.: 8 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / References: UniProt: Q39487*PLUS

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Sugars , 3 types, 17 molecules

#3: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 836 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
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: 1.91→50 Å / Num. obs: 135823 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.085 / Χ2: 0.696 / Net I/av σ(I): 12.298 / Net I/σ(I): 6.5 / Num. measured all: 532647
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.91-1.943.50.352183.6
1.94-1.983.90.317196.8
1.98-2.0240.27196.8
2.02-2.063.90.234197
2.06-2.13.90.209197.1
2.1-2.153.90.187197.2
2.15-2.240.18197.5
2.2-2.263.90.164197.4
2.26-2.333.90.15197.6
2.33-2.413.90.147197.7
2.41-2.4940.13198
2.49-2.5940.117198.1
2.59-2.713.90.102198.2
2.71-2.853.90.086198.4
2.85-3.033.90.075198.5
3.03-3.273.90.063198.7
3.27-3.593.90.055198.9
3.59-4.113.90.048199.1
4.11-5.183.90.043199.3
5.18-503.90.052199.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.1data extraction
HKL-2000data scaling
BUSTER2.11.1refinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T1X

5t1x


Resolution: 1.91→45.05 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 6809 5.01 %RANDOM
Rwork0.2091 ---
obs0.2108 135821 97.13 %-
Displacement parametersBiso max: 103.18 Å2 / Biso mean: 18.8838 Å2 / Biso min: 3.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.3137 Å2-0.9815 Å2-0.251 Å2
2--1.8786 Å2-0.0256 Å2
3----1.5649 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 1.91→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13570 0 544 835 14949
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6160SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes392HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2024HARMONIC5
X-RAY DIFFRACTIONt_it14414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1689SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16618SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14414HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg19648HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.32
X-RAY DIFFRACTIONt_other_torsion2.42
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2393 429 4.8 %
Rwork0.201 8508 -
all0.2028 8937 -
obs--97.13 %
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)
10.4090.37560.11720.83020.21370.496-0.0090.0378-0.1121-0.0480.007-0.0853-0.00040.0030.002-0.01820.01520.0083-0.0232-0.0197-0.013416.432120.3523-44.809
20.4260.0266-0.06231.01570.14520.1784-0.031-0.0096-0.01890.0530.0204-0.15870.00280.06190.0106-0.02220.005-0.0113-0.00750.0025-0.017127.671638.5014-36.3309
30.7490.22410.28910.4941-0.00390.56420.04570.0966-0.0765-0.0784-0.0373-0.02350.0460.0379-0.0085-0.03280.02740.00950.0116-0.0176-0.03485.079624.0809-90.1895
40.5864-0.00960.14780.62910.16940.0698-0.0181-0.01650.0644-0.0080.0058-0.0896-0.04360.0420.0124-0.02230.01770.00810.00930.0026-0.024711.029543.3892-79.4844
50.8287-0.0233-0.3060.22470.06731.02060.0078-0.05270.09790.09390.0103-0.0259-0.1005-0.0156-0.01810.0110.0105-0.0147-0.0465-0.0163-0.02446.490767.9848-26.0087
60.4689-0.2615-0.33370.60260.08240.21420.02830.06740.0553-0.0769-0.0282-0.0479-0.04850.0296-0.0001-0.01710.006-0.0086-0.0122-0.0028-0.008417.400558.1941-43.6466
70.6172-0.1229-0.2630.22670.19490.62010.0582-0.01220.10040.0134-0.0065-0.0176-0.0356-0.0011-0.0517-0.01020.01870.0081-0.0289-0.0162-0.0094-17.430964.5821-66.3073
80.8055-0.3238-0.60660.64130.18560.43660.06970.11980.1213-0.108-0.0366-0.0411-0.06820.0275-0.033-0.02450.02340.0012-0.0030.0073-0.0233-4.200260.3729-84.5501
91.7319-0.13310.04150.46140.11910.4763-0.0424-0.0404-0.14690.09010.0281-0.02050.05240.05470.01430.00180.0063-0.0007-0.0423-0.0036-0.03127.290616.3342-22.3065
100.886-0.384-0.36030.71060.03010.1575-0.0040.0754-0.1292-0.0251-0.0280.08330.0409-0.09320.032-0.0232-0.00620.0067-0.0055-0.0213-0.0239-12.878924.2281-29.5696
110.08120.2380.06210.945-0.50030.9817-0.00510.0089-0.00330.06190.0480.2114-0.0449-0.1007-0.0429-0.0290.01990.0021-0.023-0.0005-0.0016-14.887161.507-36.2475
120.21970.0681-0.30761.4898-0.60810.30540.0176-0.07750.0520.19020.0390.1839-0.0238-0.071-0.0565-0.01390.00650.0281-0.0085-0.0092-0.0303-16.830445.3397-20.1741
131.7619-0.43670.20770.27180.08820.5948-0.0549-0.05-0.22080.10620.04630.09180.07390.05390.0086-0.02450.02080.0197-0.03430.0173-0.013-1.660914.6719-68.5176
141.4027-0.421-0.37590.66690.34090.1289-0.04760.054-0.3401-0.0291-0.06070.1350.05-0.11060.1083-0.0581-0.00480.012-0.0249-0.03040.0225-23.531217.256-74.8695
150.33920.3297-0.28471.0775-0.49531.06310.01640.03590.0074-0.0680.00640.15-0.0468-0.1007-0.0229-0.0530.0252-0.01010.015-0.025-0.0262-35.853153.0741-77.9771
160.677-0.1296-0.34271.4716-0.05470.1648-0.0112-0.0665-0.07430.1515-0.03490.13620.0841-0.04390.0462-0.0421-0.00510.0114-0.004-0.0201-0.0237-33.222635.3333-63.6257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 108}A1 - 108
2X-RAY DIFFRACTION2{B|1 - 109}B1 - 109
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 - 109}F1 - 109
7X-RAY DIFFRACTION7{G|1 - 108}G1 - 108
8X-RAY DIFFRACTION8{H|1 - 109}H1 - 109
9X-RAY DIFFRACTION9{I|1 - 108}I1 - 108
10X-RAY DIFFRACTION10{J|1 - 109}J1 - 109
11X-RAY DIFFRACTION11{K|1 - 108}K1 - 108
12X-RAY DIFFRACTION12{L|1 - 109}L1 - 109
13X-RAY DIFFRACTION13{M|1 - 108}M1 - 108
14X-RAY DIFFRACTION14{N|1 - 109}N1 - 109
15X-RAY DIFFRACTION15{O|1 - 108}O1 - 108
16X-RAY DIFFRACTION16{P|1 - 109}P1 - 109

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