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- PDB-3o5w: Binding of kinetin in the active site of mistletoe lectin I -

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Basic information

Entry
Database: PDB / ID: 3o5w
TitleBinding of kinetin in the active site of mistletoe lectin I
Components(Beta-galactoside-specific lectin 1 chain ...) x 2
KeywordsHYDROLASE / microgravity / cytokinin / active site / Viscum album / Ribosome Inactivating Proteins / kinetin
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
triacetyl-beta-chitotriose / N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE / Beta-galactoside-specific lectin 1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMalecki, P.H. / Meyer, A. / Rypniewski, W. / Szymanski, M. / Barciszewski, J. / Betzel, C.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Binding of the plant hormone kinetin in the active site of Mistletoe Lectin I from Viscum album.
Authors: Malecki, P.H. / Rypniewski, W. / Szymanski, M. / Barciszewski, J. / Meyer, A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / diffrn_source / entity / entity_name_com / exptl_crystal_grow / 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_struct_special_symmetry / 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.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.id / _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 / _exptl_crystal_grow.method / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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 2.1Nov 1, 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 isoform 1
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,29716
Polymers56,5512
Non-polymers2,74614
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-18 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.573, 107.573, 310.633
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-49-

HOH

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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 isoform 1 / Beta-galactoside-specific lectin I / Viscumin / Beta-galactoside-specific lectin I chain A isoform ...Beta-galactoside-specific lectin I / Viscumin / Beta-galactoside-specific lectin I chain A isoform 1 / ML-I A / MLA / rRNA N-glycosidase


Mass: 27881.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / Tissue: semiparasitic plant / References: UniProt: P81446, rRNA N-glycosylase
#2: Protein Beta-galactoside-specific lectin 1 chain B / Beta-galactoside-specific lectin I / Viscumin / Beta-galactoside-specific lectin 1 chain B / Beta- ...Beta-galactoside-specific lectin I / Viscumin / Beta-galactoside-specific lectin 1 chain B / Beta-galactoside-specific lectin I chain B / ML-I B / MLB


Mass: 28670.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / Tissue: semiparasitic plant / References: UniProt: P81446, rRNA N-glycosylase

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Sugars , 3 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.: 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#6: 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.: 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

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Non-polymers , 4 types, 320 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-H35 / N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE / Kinetin


Mass: 215.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N5O / Comment: hormone*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT THE PLANT PROTEINS CAN DIFFER IN SOME CODONS DEPENDING ON THE SEASON AND ON ...THE AUTHORS STATE 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.59 Å3/Da / Density % sol: 73.19 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 2.5
Details: 1.0M ammonium sulphate, 0.2M glycine/HCl, pH 2.5, counter diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8162 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 30058 / Num. obs: 30058 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.7-2.759.1199
2.75-2.89.1199
2.8-2.859.1199.10.899
2.85-2.919.1199.20.828
2.91-2.979.1199.30.668
2.97-3.049.1199.20.583
3.04-3.129199.20.465
3.12-3.29199.30.381
3.2-3.299.1199.30.314
3.29-3.49199.30.255
3.4-3.529199.40.229
3.52-3.669199.10.165
3.66-3.838.9199.60.132
3.83-4.038.9199.50.109
4.03-4.288.8199.40.082
4.28-4.68.8199.50.074
4.6-5.068.7199.50.072
5.06-5.778.6199.40.081
5.77-7.228.4199.40.08
7.22-207.9199.10.036

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2T

1m2t


Resolution: 2.7→19.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.481 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22586 1517 5 %RANDOM
Rwork0.17409 ---
obs0.17669 28527 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.371 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20.76 Å20 Å2
2--1.52 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 181 310 4413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9845709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0324.121182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3315627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6511529
X-RAY DIFFRACTIONr_chiral_restr0.1270.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213149
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6681.52528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29324092
X-RAY DIFFRACTIONr_scbond_it2.2431660
X-RAY DIFFRACTIONr_scangle_it3.6174.51617
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 118 -
Rwork0.317 2026 -
obs--98.71 %
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)
13.21511.35911.56151.89680.86134.10810.01220.8294-0.384-0.23730.2533-0.4302-0.04870.6085-0.26550.15640.0843-0.01780.3975-0.15820.2282-3.85931.597-24.866
22.40020.76011.55421.17430.78391.67310.04340.4340.0348-0.07580.0010.0742-0.1240.1172-0.04440.14780.0181-0.05840.2059-0.02980.0908-12.81138.689-16.409
31.2335-0.91352.394411.40893.11373.5686-0.0611-0.0169-0.17920.0680.23060.9174-0.25690.0818-0.16960.1755-0.1203-0.10130.21470.03710.1554-3.60545.775-5.157
44.51541.2095-1.31432.7079-0.12684.29710.09010.42730.3788-0.58780.02720.292-0.2621-0.2915-0.11730.18120.026-0.070.02960.02480.06647.99858.99710.653
52.92731.86851.40592.56541.14661.28620.1575-0.0349-0.0863-0.0379-0.04720.1570.1424-0.2115-0.11020.13580.0068-0.08210.06890.01540.05980.94641.19612.984
67.6547-6.88367.164815.2467-4.90468.07520.3116-0.0085-1.36920.43750.34341.38120.7976-0.6575-0.65490.3987-0.1248-0.08680.1853-0.15740.4036-7.30624.4446.597
73.22630.17724.5738-0.62250.46789.949-0.26010.84570.1235-0.4210.20290.081-0.93890.81470.05720.3889-0.1121-0.14610.30630.06670.71033.14754.893-2.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2A120 - 219
3X-RAY DIFFRACTION3A220 - 248
4X-RAY DIFFRACTION4B249 - 315
5X-RAY DIFFRACTION5B316 - 482
6X-RAY DIFFRACTION6B483 - 510
7X-RAY DIFFRACTION7A255 - 257
8X-RAY DIFFRACTION7A500
9X-RAY DIFFRACTION7A601
10X-RAY DIFFRACTION7A801 - 802
11X-RAY DIFFRACTION7B600 - 607
12X-RAY DIFFRACTION7B1
13X-RAY DIFFRACTION7B511
14X-RAY DIFFRACTION7B800
15X-RAY DIFFRACTION7B803

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