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- PDB-2r9k: Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide -

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Entry
Database: PDB / ID: 2r9k
TitleCrystal Structure of Misteltoe Lectin I in Complex with Phloretamide
Components(Beta-galactoside-specific lectin ...) x 2
KeywordsHYDROLASE / ML-I / phloretamide / Viscum album / Glycoprotein / Lectin / Plant defense / Protein synthesis inhibitor / Toxin
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
3-(4-hydroxyphenyl)propanamide / Beta-galactoside-specific lectin 1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeyer, A. / Rypniewski, W. / Celewicz, L. / Erdmann, V.A. / Voelter, W. / Betzel, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: The mistletoe lectin I--phloretamide structure reveals a new function of plant lectins.
Authors: Meyer, A. / Rypniewski, W. / Celewicz, L. / Erdmann, V.A. / Voelter, W. / Singh, T.P. / Genov, N. / Barciszewski, J. / Betzel, C.h.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 20, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 3.0May 4, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_branch_scheme / 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_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id
Revision 3.1Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999The authors stae that the plant proteins can differ in some codons depending on the season and on ...The authors stae that the plant proteins can differ in some codons depending on the season and on the host where the mistletoe has grown.

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


Theoretical massNumber of molelcules
Total (without water)58,65217
Polymers56,3892
Non-polymers2,26315
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-76 kcal/mol
Surface area19830 Å2
2
A: Beta-galactoside-specific lectin 1
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)117,30334
Polymers112,7784
Non-polymers4,52530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area15160 Å2
ΔGint-177 kcal/mol
Surface area38940 Å2
MethodPISA
3
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules

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

A: Beta-galactoside-specific lectin 1
hetero molecules

A: Beta-galactoside-specific lectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,30334
Polymers112,7784
Non-polymers4,52530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
crystal symmetry operation6_654x-y+1,x,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area12250 Å2
ΔGint-157 kcal/mol
Surface area41850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.059, 107.059, 312.375
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-668-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
12

NCS domain segments:

Dom-ID: 1 / Component-ID: 1 / Refine code: 1

Ens-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLNGLNTHRTHRAA99 - 10599 - 105
2ALAALAGLYGLYBB480 - 500233 - 253

NCS ensembles :
ID
1
2

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Components

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

#1: Protein Beta-galactoside-specific lectin 1


Mass: 27820.066 Da / Num. of mol.: 1
Fragment: Beta-galactoside-specific lectin 1 chain A isoform 1, UNP residues 34-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Viscum album (European mistletoe) / References: UniProt: P81446*PLUS
#2: Protein Beta-galactoside-specific lectin 1 chain B / Beta-galactoside-specific lectin I chain B / ML-I B / MLB


Mass: 28568.939 Da / Num. of mol.: 1
Fragment: Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Viscum album (European mistletoe) / References: UniProt: P81446

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Sugars , 2 types, 5 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-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
DGlcpNAcb4-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+4)][D-1-deoxy-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.: 4
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 , 5 types, 82 molecules

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


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SGI / 3-(4-hydroxyphenyl)propanamide


Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 4.58 Å3/Da / Density % sol: 73.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.7→91.29 Å / Num. obs: 30327 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.6 / Rsym value: 0.473 / Net I/σ(I): 3.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2T

1m2t


Resolution: 2.7→19.74 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.263 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26704 1470 4.9 %RANDOM
Rwork0.22622 ---
obs0.22821 28628 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.964 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20.92 Å20 Å2
2--1.83 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 141 72 4124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9745630
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41124.341182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93415629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5161528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.050.023114
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22812
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5421.52580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98724105
X-RAY DIFFRACTIONr_scbond_it1.27531751
X-RAY DIFFRACTIONr_scangle_it2.0534.51525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

Ens-IDAuth asym-IDNumberTypeWeight position
1A52tight positional0.05
2B155tight positional0.05
1A52tight thermal0.5
2B155tight thermal0.5
LS refinement shellResolution: 2.696→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 90 -
Rwork0.329 2031 -
obs--99.76 %

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