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- PDB-4eb2: Crystal structure Mistletoe Lectin I from Viscum album in complex... -

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Basic information

Entry
Database: PDB / ID: 4eb2
TitleCrystal structure Mistletoe Lectin I from Viscum album in complex with n-acetyl-d-glucosamine at 1.94 A resolution.
Components(Beta-galactoside-specific lectin 1 chain ...) x 2
KeywordsHYDROLASE/SUGAR BINDING PROTEIN / Rossmann fold / ribosome-inactivating protein type II / glycoprotein / plant defense / protein synthesis inhibitor / toxin / sarcin/ricin domain / galactose binding receptor / HYDROLASE-SUGAR BINDING PROTEIN complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / DI(HYDROXYETHYL)ETHER / Beta-galactoside-specific lectin 1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsLaskov, A.A. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Crystal structure Mistletoe Lectin I from Viscum album in complex with N-acetyl-D-glucosamine at 1.94 A resolution.
Authors: Laskov, A.A. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / 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_unobs_or_zero_occ_atoms / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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: Beta-galactoside-specific lectin 1 chain A
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,76429
Polymers55,7082
Non-polymers3,05527
Water4,161231
1
A: Beta-galactoside-specific lectin 1 chain A
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules

A: Beta-galactoside-specific lectin 1 chain A
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,52858
Polymers111,4174
Non-polymers6,11154
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-14 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.058, 107.058, 311.201
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Beta-galactoside-specific lectin 1 chain ... , 2 types, 2 molecules AB

#1: Protein Beta-galactoside-specific lectin 1 chain A / Viscumin / Beta-galactoside-specific lectin I chain A / ML-I A / MLA / rRNA N-glycosidase


Mass: 27300.711 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446*PLUS, rRNA N-glycosylase
#2: Protein Beta-galactoside-specific lectin 1 chain B / Viscumin / Beta-galactoside-specific lectin I chain B / ML-I B / MLB


Mass: 28407.717 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446*PLUS

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Sugars , 2 types, 4 molecules

#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.: 1
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 254 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT BETA-GALACTOSIDE-SPECIFIC LECTIN 1 (VISCUMIN) FROM NATURAL SOURCES IS ...THE AUTHORS STATE THAT BETA-GALACTOSIDE-SPECIFIC LECTIN 1 (VISCUMIN) FROM NATURAL SOURCES IS VARIABLE IN SEQUENCE AND THAT THE SEQUENCE IN THIS ENTRY WAS IDENTIFIED FROM ELECTRON DENSITY. THE CLOSEST UNIPROT REFERENCE IS P81446 (ML1_VISAL) RESIDUES 34-482 FOR CHAIN A AND RESIDUES 302-564 FOR CHAIN B.

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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: 4.62 Å3/Da / Density % sol: 73.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 0.01 M sodium acetate, 25% saturated ammonium sulfate, 0.1 M glycin/HCl buffer, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 23, 2011
RadiationMonochromator: horizontally focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.94→29.5 Å / Num. all: 78881 / Num. obs: 77457 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.172 / Net I/σ(I): 13.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SZ6

1sz6


Resolution: 1.94→7.998 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.33 / σ(F): 1.99 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 3809 5 %
Rwork0.1803 --
obs0.1827 76180 98.25 %
all-77457 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.939 Å2 / ksol: 0.46 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.019 Å2-0 Å2-0 Å2
2--1.019 Å2-0 Å2
3----2.0381 Å2
Refinement stepCycle: LAST / Resolution: 1.94→7.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 177 231 4324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084234
X-RAY DIFFRACTIONf_angle_d1.0115727
X-RAY DIFFRACTIONf_dihedral_angle_d13.3441545
X-RAY DIFFRACTIONf_chiral_restr0.071654
X-RAY DIFFRACTIONf_plane_restr0.004739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.96420.4781260.4382395X-RAY DIFFRACTION90
1.9642-1.98970.36571400.34222673X-RAY DIFFRACTION98
1.9897-2.01650.36081390.31122641X-RAY DIFFRACTION98
2.0165-2.04480.36911370.29962585X-RAY DIFFRACTION98
2.0448-2.07480.32351380.27962624X-RAY DIFFRACTION97
2.0748-2.10670.27361370.25222613X-RAY DIFFRACTION97
2.1067-2.14060.29851380.23722624X-RAY DIFFRACTION97
2.1406-2.17680.32191380.25272607X-RAY DIFFRACTION97
2.1768-2.21550.34921360.27052598X-RAY DIFFRACTION97
2.2155-2.25720.39351380.27012606X-RAY DIFFRACTION97
2.2572-2.30220.31171390.26022647X-RAY DIFFRACTION98
2.3022-2.3510.31941410.22412680X-RAY DIFFRACTION98
2.351-2.40430.26211400.19612658X-RAY DIFFRACTION99
2.4043-2.46270.25431400.17132667X-RAY DIFFRACTION99
2.4627-2.52720.23141410.17832667X-RAY DIFFRACTION98
2.5272-2.59910.22531400.17962662X-RAY DIFFRACTION98
2.5991-2.67990.28271420.19632695X-RAY DIFFRACTION98
2.6799-2.77190.21261410.18982689X-RAY DIFFRACTION100
2.7719-2.87790.2491440.16712729X-RAY DIFFRACTION100
2.8779-3.00220.20551440.16082741X-RAY DIFFRACTION100
3.0022-3.15130.23721450.15862754X-RAY DIFFRACTION100
3.1513-3.33520.21071440.17622739X-RAY DIFFRACTION100
3.3352-3.57130.21831470.16322780X-RAY DIFFRACTION100
3.5713-3.89260.18761450.1472756X-RAY DIFFRACTION100
3.8926-4.37340.15321470.1222788X-RAY DIFFRACTION100
4.3734-5.23890.14761490.13032832X-RAY DIFFRACTION99
5.2389-7.99760.23061530.19462921X-RAY DIFFRACTION99

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