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- PDB-5z3i: Crystal Structure of Abrin A chain (Recombinant) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5z3i
TitleCrystal Structure of Abrin A chain (Recombinant) in complex with Adenine at 1.65 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
ADENINE / Abrin-a / Abrin A-chain
Similarity search - Component
Biological speciesAbrus precatorius (Indian licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Assembly

Deposited unit
A: Abrin A-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8422
Polymers29,7071
Non-polymers1351
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area10770 Å2
Unit cell
Length a, b, c (Å)41.760, 73.500, 81.880
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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.65→41.76 Å / Num. obs: 31092 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 17.6 / Num. measured all: 212904 / Scaling rejects: 220
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.6850.60515250.8720.2980.67799.9
9.04-41.765.20.0192000.9990.0090.02187

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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: 1.65→40.94 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1476 4.76 %RANDOM
Rwork0.1767 ---
obs0.1777 31026 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 35.4494 Å2 / Biso min: 14.47 Å2
Refinement stepCycle: final / Resolution: 1.65→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 10 159 2060
Biso mean--28.82 38.97 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051957
X-RAY DIFFRACTIONf_angle_d0.6522672
X-RAY DIFFRACTIONf_chiral_restr0.047308
X-RAY DIFFRACTIONf_plane_restr0.004351
X-RAY DIFFRACTIONf_dihedral_angle_d14.2341170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.70330.34631330.270226412774100
1.7033-1.76410.29551250.257426542779100
1.7641-1.83480.26291140.221626722786100
1.8348-1.91830.2411220.204926712793100
1.9183-2.01940.21971340.193726362770100
2.0194-2.14590.2391220.177926792801100
2.1459-2.31160.20651410.176126802821100
2.3116-2.54420.17071340.16626762810100
2.5442-2.91230.20211530.174426872840100
2.9123-3.66880.16781490.170427372886100
3.6688-40.95250.17731490.15892817296699
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)
16.65920.19042.68423.1873-0.65614.04890.4568-0.5437-0.47250.4592-0.1505-0.01550.2404-0.1862-0.26090.2423-0.0192-0.03030.20930.0880.2161-39.475877.038521.9382
25.33592.01470.9284.34590.13381.28840.0432-0.27380.30170.19430.06090.26140.0204-0.2189-0.09650.16450.01040.030.21320.02130.1148-44.105187.013818.3846
34.0912-0.8205-1.6114.9341.71063.31660.06420.40860.5966-0.2626-0.06390.1894-0.2718-0.231-0.05230.20190.0051-0.02510.19720.06370.2433-39.330497.935412.8843
44.3620.75420.91684.97821.20757.8137-0.07140.15770.1174-0.04210.007-0.4421-0.26410.2340.0680.1495-0.0327-0.00650.23860.04280.3256-25.860989.50212.8989
54.7417-0.28310.71534.4431-0.34063.4195-0.01760.2352-0.4564-0.0338-0.0424-0.5890.1620.25040.06890.1573-0.0030.00790.1858-0.00220.2363-30.927180.10411.4994
62.82322.33751.17024.66261.28291.7475-0.14710.7388-0.174-0.91110.46970.21370.2125-0.1537-0.26810.3825-0.1182-0.07450.37650.0260.1833-44.197777.16391.7576
70.8565-1.0453-0.11813.6223-0.96491.82360.35610.2304-0.6498-1.02820.4259-0.02410.89550.3174-0.70190.8488-0.1669-0.12680.7627-0.23390.4145-44.577270.2204-3.8527
82.2970.6263-1.66124.77180.06795.8074-0.17380.7415-0.8696-0.69520.16940.25370.6427-0.6280.07940.4148-0.1452-0.07550.4173-0.06250.392-48.471271.6783.4832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 33 )A3 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 80 )A34 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 120 )A81 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 147 )A121 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 188 )A148 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 207 )A189 - 207
7X-RAY DIFFRACTION7chain 'A' and (resid 208 through 225 )A208 - 225
8X-RAY DIFFRACTION8chain 'A' and (resid 226 through 249 )A226 - 249

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