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- PDB-2zr1: Agglutinin from Abrus Precatorius -

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Basic information

Entry
Database: PDB / ID: 2zr1
TitleAgglutinin from Abrus Precatorius
Components
  • Agglutinin-1 chain A
  • Agglutinin-1 chain B
KeywordsPLANT PROTEIN / RIBOSOME-INACTIVATING PROTEIN / IMMUNOTOXIN / AGGLUTININ ABRIN / Glycoprotein / Hydrolase / Lectin / Plant defense / Protein synthesis inhibitor / Pyrrolidone carboxylic acid / Toxin
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / heterophilic cell-cell adhesion / 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 conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...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 conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / 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
Biological speciesAbrus precatorius (Indian licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCheng, J. / Lu, T.H. / Liu, C.L. / Lin, J.Y.
Citation
Journal: J.Biomed.Sci. / Year: 2010
Title: A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure
Authors: Cheng, J. / Lu, T.H. / Liu, C.L. / Lin, J.Y.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin
Authors: Bagaria, A. / Surendranath, K. / Ramagopal, U.A. / Ramakumar, S. / Karande, A.A.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Primary structure and function analysis of the Abrus precatorius agglutinin A chain by site-directed mutagenesis. Pro(199) Of amphiphilic alpha-helix H impairs protein synthesis inhibitory activity
Authors: Liu, C.-L. / Tsai, C.-C. / Lin, S.-C. / Wang, L.-I. / Hsu, C.-I. / Hwang, M.-J. / Lin, J.-Y.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization of agglutinin from the seeds of Abrus precatorius
Authors: Panneerselvam, K. / Lin, S.-C. / Liu, C.-L. / Liaw, Y.-C. / Lin, J.-Y. / Lu, T.-H.
#4: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of abrin-a at 2.14 A
Authors: Tahirov, T.H. / Lu, T.-H. / Liaw, Y.-C. / Chen, Y.-L. / Lin, J.-Y.
History
DepositionAug 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agglutinin-1 chain A
B: Agglutinin-1 chain B
C: Agglutinin-1 chain A
D: Agglutinin-1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0067
Polymers117,3424
Non-polymers6643
Water3,045169
1
A: Agglutinin-1 chain A
B: Agglutinin-1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1144
Polymers58,6712
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-11 kcal/mol
Surface area20660 Å2
MethodPISA
2
C: Agglutinin-1 chain A
D: Agglutinin-1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8923
Polymers58,6712
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-17 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.050, 137.050, 214.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Agglutinin-1 chain A / Agglutinin I / AAG-A


Mass: 28664.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Abrus precatorius (Indian licorice) / References: UniProt: Q9M6E9, rRNA N-glycosylase
#2: Protein Agglutinin-1 chain B / Agglutinin I / AAG-B


Mass: 30006.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Abrus precatorius (Indian licorice) / References: UniProt: Q9M6E9
#3: 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.: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.45 Å3/Da / Density % sol: 72.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 6.5% PEG 8000, 1% SODIUM AZIDE, 0.1M TRIS BUFFER, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 19, 2004
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→30 Å / Num. obs: 73976 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 50.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 11.9
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.36 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNS2.02refinement
HKL-2000data reduction
HKL-2000data scaling
CNS2.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ABR

1abr


Resolution: 2.6→19.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 574723.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6301 10 %RANDOM
Rwork0.199 ---
obs0.199 63111 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 221.453 Å2 / ksol: 0.34085 e/Å3
Displacement parametersBiso mean: 49.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2--1.81 Å20 Å2
3----3.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 42 169 8271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.871.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it2.872
X-RAY DIFFRACTIONc_scangle_it3.92.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 1018 9.8 %
Rwork0.211 9375 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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