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- PDB-5z37: Crystal Structure of Abrin A chain (Recombinant) at 1.3 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5z37
TitleCrystal Structure of Abrin A chain (Recombinant) at 1.3 Angstroms
ComponentsAbrin A-chain
KeywordsHYDROLASE / Ribosome Inactivating Protein
Function / homology
Function and homology information


galactose binding / rRNA N-glycosylase / rRNA N-glycosylase activity / positive regulation of endocytosis / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Abrin-a / Abrin A-chain
Similarity search - Component
Biological speciesAbrus precatorius (Indian licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBansia, H. / Karande, A.A. / Ramakumar, S.
CitationJournal: FEBS J. / Year: 2019
Title: Structural basis for neutralization of cytotoxic abrin by monoclonal antibody D6F10.
Authors: Bansia, H. / Bagaria, S. / Karande, A.A. / Ramakumar, S.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abrin A-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7762
Polymers29,7071
Non-polymers691
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint1 kcal/mol
Surface area11110 Å2
Unit cell
Length a, b, c (Å)41.660, 73.820, 82.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Abrin A-chain


Mass: 29707.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Abrus precatorius (Indian licorice) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DM12, UniProt: P11140*PLUS
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the conflict (Y85H) is due to an ISOFORM OF Q7DM12 (ABRIN-A), but the isoform ...Authors state that the conflict (Y85H) is due to an ISOFORM OF Q7DM12 (ABRIN-A), but the isoform has not been reported in UniProt DB. FOR REFERENCE : Hung, C. H., Lee, M. C., Lee, T. C. & Lin, J. Y. (1993) Primary structure of three distinct isoabrins determined by cDNA sequencing : conservation and significance, J. Mol. Biol. 229,263 - 267

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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: 2.3 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 295.15 K / Method: microbatch / pH: 6.5 / Details: 0.2M Magnesium Chloride, 20% PEG 8K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→27.63 Å / Num. obs: 57887 / % possible obs: 91.7 % / Redundancy: 7 % / Biso Wilson estimate: 13.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 18.3 / Num. measured all: 405186 / Scaling rejects: 365
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.3-1.326.70.90130260.8320.3650.97499.1
7.12-27.635.80.0154200.9990.0070.01792.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABR

1abr


Resolution: 1.3→27.198 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.14
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 2916 5.05 %RANDOM
Rwork0.1562 ---
obs0.1573 57769 91.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.09 Å2 / Biso mean: 21.3698 Å2 / Biso min: 9.71 Å2
Refinement stepCycle: final / Resolution: 1.3→27.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 5 275 2178
Biso mean--21.34 29.96 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051994
X-RAY DIFFRACTIONf_angle_d0.7592728
X-RAY DIFFRACTIONf_chiral_restr0.069314
X-RAY DIFFRACTIONf_plane_restr0.005360
X-RAY DIFFRACTIONf_dihedral_angle_d16.422724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32130.2191450.19382746289199
1.3213-1.34410.24241510.18672838298999
1.3441-1.36850.25761430.19112769291299
1.3685-1.39490.21861560.16912804296099
1.3949-1.42330.22771600.1742771293199
1.4233-1.45430.19521100.16442027213772
1.4543-1.48810.21171150.15222094220974
1.4881-1.52530.20971380.13327562894100
1.5253-1.56660.17131310.12921702301100
1.5666-1.61260.17341310.127928642995100
1.6126-1.66470.18251560.126728062962100
1.6647-1.72420.16651460.131828422988100
1.7242-1.79320.21391550.136428232978100
1.7932-1.87480.19211710.143328343005100
1.8748-1.97360.2231690.19181381145048
1.9736-2.09720.17351370.14422510264788
2.0972-2.25910.18061290.160726812810100
2.2591-2.48630.17741450.143327072852100
2.4863-2.84570.13851320.1512740287294
2.8457-3.5840.17331530.16492818297196
3.584-27.20410.16891430.16862872301593

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