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- PDB-5z3j: Crystal Structure of Abrin A chain (Recombinant) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5z3j
TitleCrystal Structure of Abrin A chain (Recombinant) in complex with Nicotinamide at 1.7 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 / 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 / NICOTINAMIDE / Abrin-a / Abrin A-chain
Similarity search - Component
Biological speciesAbrus precatorius (Indian licorice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 8, 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

Downloads & links

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Assembly

Deposited unit
A: Abrin A-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8983
Polymers29,7071
Non-polymers1912
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint8 kcal/mol
Surface area10760 Å2
Unit cell
Length a, b, c (Å)41.660, 74.080, 82.480
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 / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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 the 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: 2.32 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 295.15 K / Method: microbatch / pH: 6.5 / Details: 20% PEG 8000, 0.2M Magnesium Chloride, Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→23.66 Å / Num. obs: 26038 / % possible obs: 90.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.736.70.66615300.8050.2830.726100
9-23.665.80.0412330.9920.020.04695.5

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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: 1.7→23.656 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1261 4.87 %RANDOM
Rwork0.1997 ---
obs0.2009 25908 89.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.35 Å2 / Biso mean: 27.2545 Å2 / Biso min: 11.68 Å2
Refinement stepCycle: final / Resolution: 1.7→23.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 14 197 2093
Biso mean--23.22 31.36 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031950
X-RAY DIFFRACTIONf_angle_d0.5362658
X-RAY DIFFRACTIONf_chiral_restr0.043305
X-RAY DIFFRACTIONf_plane_restr0.003350
X-RAY DIFFRACTIONf_dihedral_angle_d13.1271165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.76810.31111430.309430233166100
1.7681-1.84850.31411530.28929873140100
1.8485-1.94590.3643850.32611861194662
1.9459-2.06780.20951410.20432576271786
2.0678-2.22730.22371380.19832644278288
2.2273-2.45120.30161520.23642634278687
2.4512-2.80550.20231540.18222869302394
2.8055-3.53270.21591530.17662982313596
3.5327-23.65820.1651420.16583071321395
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)
15.60830.98673.32193.7379-0.16475.09880.1775-0.305-0.34590.4012-0.0616-0.27860.1137-0.0806-0.11930.1695-0.0127-0.02890.12060.02590.1466-39.03677.890122.0332
24.23432.09882.5166.47260.36682.3637-0.0764-0.22630.46530.12260.13690.90160.067-0.2806-0.03420.1252-0.02840.03530.23410.07760.2346-54.907283.947214.8592
36.08450.41160.83413.7256-0.05651.76680.0599-0.48120.01480.4260.0177-0.1394-0.0832-0.0841-0.09370.1666-0.00260.01070.13230.01180.1015-37.794190.685820.9335
43.6278-0.4431-0.81464.19080.84571.24980.08130.21140.3248-0.12640.00850.1759-0.1371-0.1479-0.07920.1491-0.0114-0.00710.12480.04220.1421-39.072698.887612.8841
52.98810.97330.79043.6136-0.27685.1751-0.08530.0871-0.118-0.0402-0.0594-0.5935-0.14950.18730.13520.1195-0.02140.00770.17250.02310.277-25.685790.204112.9781
65.3224.8344-0.70169.3664-2.00333.1974-0.14520.13440.06330.00630.06-0.3346-0.10880.08360.1010.0950.00860.0140.1469-0.01450.1279-32.164388.239711.3526
78.04412.20470.77433.51771.28592.3668-0.07010.0316-1.0664-0.10340.0173-1.33280.21520.29290.01630.2140.00830.06630.13530.01780.5083-29.529574.205912.2103
83.01382.0802-1.26864.05850.35441.2072-0.38210.87480.3867-1.42340.5966-0.0890.1445-0.0804-0.14060.4046-0.1417-0.01650.2918-0.00460.0722-43.944278.0282.0108
97.59820.4547-0.31240.94820.24081.45830.38830.3502-0.4485-1.08980.6073-0.34660.07880.1542-0.39650.8347-0.33980.10090.6251-0.40010.0597-45.225271.304-3.5267
100.071-0.10560.65320.1398-0.80114.7113-0.01470.1979-0.4314-1.01110.5817-0.20340.70940.1198-0.42550.6875-0.1860.09040.4727-0.13350.3577-44.632867.6970.3549
112.9120.1302-2.67876.12760.22642.46070.07780.1785-0.1153-0.63730.11370.77130.1153-0.3711-0.10340.1831-0.0743-0.06220.24330.0630.2481-52.84378.07917.7951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )A4 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 50 )A34 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 80 )A51 - 80
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 120 )A81 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 147 )A121 - 147
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 167 )A148 - 167
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 188 )A168 - 188
8X-RAY DIFFRACTION8chain 'A' and (resid 189 through 207 )A189 - 207
9X-RAY DIFFRACTION9chain 'A' and (resid 208 through 225 )A208 - 225
10X-RAY DIFFRACTION10chain 'A' and (resid 226 through 239 )A226 - 239
11X-RAY DIFFRACTION11chain 'A' and (resid 240 through 249 )A240 - 249

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