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- PDB-1yf8: Crystal structure of Himalayan mistletoe RIP reveals the presence... -

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Entry
Database: PDB / ID: 1yf8
TitleCrystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site
Components(Beta-galactoside-specific lectin ...) x 2
KeywordsHYDROLASE / Himalayan mistletoe / ribosome inactivating protein / Viscum album / natural inhibitor / sugar-binding site
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
beta-lactose / beta-D-galactopyranose / 2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID / Beta-galactoside-specific lectin 4
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsMishra, V. / Bilgrami, S. / Sharma, R.S. / Kaur, P. / Yadav, S. / Betzel, C. / Babu, C.R. / Singh, T.P.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site.
Authors: Mishra, V. / Bilgrami, S. / Sharma, R.S. / Kaur, P. / Yadav, S. / Krauspenhaar, R. / Betzel, C. / Voelter, W. / Babu, C.R. / Singh, T.P.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 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 / database_PDB_caveat / diffrn_source / 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_chiral / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 25, 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 4
B: Beta-galactoside-specific lectin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,27910
Polymers54,2012
Non-polymers3,0798
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint22 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.422, 109.422, 309.798
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 ... , 2 types, 2 molecules AB

#1: Protein Beta-galactoside-specific lectin 4 / ribosome-inactivating protein / MISTLETOE LECTIN


Mass: 26566.869 Da / Num. of mol.: 1 / Fragment: residues 1-240 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / Strain: Himalayan V.album / References: UniProt: Q6ITZ3, rRNA N-glycosylase
#2: Protein Beta-galactoside-specific lectin 4 / ribosome-inactivating protein / MISTLETOE LECTIN


Mass: 27633.693 Da / Num. of mol.: 1 / Fragment: residues 1-255 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / Strain: Himalayan V.album / References: UniProt: Q6ITZ3, rRNA N-glycosylase

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Sugars , 6 types, 7 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: Polysaccharide beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Altp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#9: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 108 molecules

#8: Chemical ChemComp-P6C / 2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID


Mass: 233.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11N5O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 4.7 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: NaCl, Ammonium Sulphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8453 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 26570 / % possible obs: 95.8 % / Rsym value: 0.057 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 33.6 / Num. unique all: 1333

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MIR
Starting model: 1pc8

1pc8


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 27.281 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28712 1301 5.1 %RANDOM
Rwork0.23443 ---
obs0.23715 26570 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 85.76 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å22.41 Å20 Å2
2--4.83 Å20 Å2
3----7.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 205 107 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224101
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2271.9955594
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.185493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94924.396182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.33515610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.951527
X-RAY DIFFRACTIONr_chiral_restr0.1660.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023057
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2960.22024
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.22763
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7931.52496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40323953
X-RAY DIFFRACTIONr_scbond_it2.00331850
X-RAY DIFFRACTIONr_scangle_it3.1974.51641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.867 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 84
Rwork0.321 1769
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)
12.6732-1.6198-1.18142.15640.9272.1131-0.124-0.41320.15980.260.1758-0.0992-0.11540.2182-0.0518-0.16880.04040.05020.2937-0.0685-0.19348.40457.185219.6104
23.295-1.7947-0.85882.89791.03342.33420.0327-0.21950.0520.02420.06130.2364-0.2233-0.2717-0.094-0.3151-0.14820.09160.0348-0.0443-0.327958.871249.6849-11.4339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2401 - 240
2X-RAY DIFFRACTION2BB1 - 2551 - 255

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