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- PDB-6tt9: rTBL Recombinant Lectin From Tepary Bean -

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Basic information

Entry
Database: PDB / ID: 6tt9
TitlerTBL Recombinant Lectin From Tepary Bean
ComponentsPhytohemagglutininPhytohaemagglutinin
KeywordsSUGAR BINDING PROTEIN / bean / cancer type glycans / tetrameric protein / leguminous lectin / b1-6 branched N-glycans
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Legume lectin / 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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
HEXANE / : / Phytohemagglutinin
Similarity search - Component
Biological speciesPhaseolus acutifolius (tepary bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMartinez Alarcon, D. / Varrot, A.
Funding support Mexico, France, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CB-2014-01-241181 Mexico
European Commission765581 France
CitationJournal: Biomolecules / Year: 2020
Title: Recombinant Lectin from Tepary Bean (Phaseolus acutifolius) with Specific Recognition for Cancer-Associated Glycans: Production, Structural Characterization, and Target Identification.
Authors: Martinez-Alarcon, D. / Varrot, A. / Fitches, E. / Gatehouse, J.A. / Cao, M. / Pyati, P. / Blanco-Labra, A. / Garcia-Gasca, T.
History
DepositionDec 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn
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.occupancy / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Phytohemagglutinin
BBB: Phytohemagglutinin
CCC: Phytohemagglutinin
DDD: Phytohemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,15921
Polymers110,0294
Non-polymers4,13017
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-18 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.572, 64.472, 67.590
Angle α, β, γ (deg.)96.352, 101.952, 97.268
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains AAA CCC
33Chains AAA DDD
44Chains BBB CCC
55Chains BBB DDD
66Chains CCC DDD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Phytohemagglutinin / Phytohaemagglutinin


Mass: 27507.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus acutifolius (tepary bean) / Cell line (production host): SMD1168H / Production host: Komagataella pastoris (fungus) / References: UniProt: Q40750

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 517 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mn
#7: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H14
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45 % / Description: THICK PLATE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% Peg smear low 100mM Tris pH 7.5 PEG to 30% for cryoprotection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→32.732 Å / Num. obs: 73400 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.049 / Rsym value: 0.088 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4491 / CC1/2: 0.902 / Rpim(I) all: 0.372 / Rsym value: 0.649 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fat

1fat


Resolution: 1.9→32.73 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.11 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2132 3646 4.968 %
Rwork0.1692 --
all0.171 --
obs-73390 99.697 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.385 Å2-2.801 Å2-2.541 Å2
2--0.265 Å20.713 Å2
3----0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7015 0 260 504 7779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176742
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.64610363
X-RAY DIFFRACTIONr_angle_other_deg1.4451.57415711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6775949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06223.127355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0231532
X-RAY DIFFRACTIONr_chiral_restr0.0910.21081
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021555
X-RAY DIFFRACTIONr_nbd_refined0.190.21247
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.26265
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23661
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.23579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2434
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1420.22
X-RAY DIFFRACTIONr_metal_ion_refined0.110.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.237
X-RAY DIFFRACTIONr_nbd_other0.2430.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.218
X-RAY DIFFRACTIONr_mcbond_it3.4392.8783769
X-RAY DIFFRACTIONr_mcbond_other3.4292.8773768
X-RAY DIFFRACTIONr_mcangle_it4.474.2864721
X-RAY DIFFRACTIONr_mcangle_other4.4714.2874722
X-RAY DIFFRACTIONr_scbond_it4.2623.2783799
X-RAY DIFFRACTIONr_scbond_other4.2613.2793800
X-RAY DIFFRACTIONr_scangle_it5.9734.7735640
X-RAY DIFFRACTIONr_scangle_other5.9724.7735641
X-RAY DIFFRACTIONr_lrange_it7.20934.9418015
X-RAY DIFFRACTIONr_lrange_other7.17334.7367923
X-RAY DIFFRACTIONr_ncsr_local_group_10.0860.057271
X-RAY DIFFRACTIONr_ncsr_local_group_20.0780.057420
X-RAY DIFFRACTIONr_ncsr_local_group_30.0770.057317
X-RAY DIFFRACTIONr_ncsr_local_group_40.0850.057261
X-RAY DIFFRACTIONr_ncsr_local_group_50.0930.057226
X-RAY DIFFRACTIONr_ncsr_local_group_60.0890.057111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3212680.3035137X-RAY DIFFRACTION98.8298
1.949-2.0020.2872400.2574987X-RAY DIFFRACTION99.4482
2.002-2.060.242530.2284868X-RAY DIFFRACTION99.5916
2.06-2.1230.252630.2024743X-RAY DIFFRACTION99.6417
2.123-2.1930.2382730.184555X-RAY DIFFRACTION99.6491
2.193-2.2690.2142430.1674412X-RAY DIFFRACTION99.7429
2.269-2.3550.2082130.1454274X-RAY DIFFRACTION99.822
2.355-2.450.2192000.1524167X-RAY DIFFRACTION99.8171
2.45-2.5580.2061910.1583995X-RAY DIFFRACTION99.9284
2.558-2.6820.1981700.1663815X-RAY DIFFRACTION99.9749
2.682-2.8270.211970.1593602X-RAY DIFFRACTION99.9737
2.827-2.9970.1941880.1593417X-RAY DIFFRACTION100
2.997-3.2020.2321630.1733216X-RAY DIFFRACTION99.9704
3.202-3.4550.2141700.172965X-RAY DIFFRACTION100
3.455-3.7810.221490.1692760X-RAY DIFFRACTION99.897
3.781-4.220.171150.1392512X-RAY DIFFRACTION99.9619
4.22-4.860.1461140.1142193X-RAY DIFFRACTION99.8701
4.86-5.9190.1981140.1481828X-RAY DIFFRACTION99.6408
5.919-8.2370.247760.1961471X-RAY DIFFRACTION99.8709

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