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- PDB-4q2v: Crystal Structure of Ricin A chain complexed with Baicalin inhibitor -

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Basic information

Entry
Database: PDB / ID: 4q2v
TitleCrystal Structure of Ricin A chain complexed with Baicalin inhibitor
ComponentsRicin
KeywordsHydrolase/Hydrolase inhibitor / mixed alpha/beta structure / ribosome-inactivating / baicalin complex / ribosome / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / 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 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsDeng, X. / Li, X. / Dong, J. / Chen, Y.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Baicalin inhibits the lethality of ricin in mice by inducing protein oligomerization.
Authors: Dong, J. / Zhang, Y. / Chen, Y. / Niu, X. / Zhang, Y. / Li, R. / Yang, C. / Wang, Q. / Li, X. / Deng, X.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7022
Polymers31,2551
Non-polymers4461
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.197, 68.197, 133.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein Ricin / Ricin toxin chain A


Mass: 31255.213 Da / Num. of mol.: 1 / Fragment: Ricin A chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pGex-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-0XE / 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl beta-D-glucopyranosiduronic acid / Baicalin


Mass: 446.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulphate, 0.1M sodium acetate, 10% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2013 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.198→50 Å / Num. all: 16740 / Num. obs: 16723 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 34.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 5.3 / Num. unique all: 794 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RTJ

3rtj


Resolution: 2.198→39.066 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 842 5.05 %RANDOM
Rwork0.2107 ---
all0.2123 16723 --
obs0.2123 16668 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.635 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 103.22 Å2 / Biso mean: 46.1103 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.8761 Å2-0 Å20 Å2
2---0.8761 Å20 Å2
3---1.7521 Å2
Refinement stepCycle: LAST / Resolution: 2.198→39.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 32 56 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092126
X-RAY DIFFRACTIONf_angle_d1.0522899
X-RAY DIFFRACTIONf_chiral_restr0.069323
X-RAY DIFFRACTIONf_plane_restr0.005380
X-RAY DIFFRACTIONf_dihedral_angle_d15.57769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1983-2.3360.32591580.248825232681
2.336-2.51630.24311450.229625812726
2.5163-2.76950.29641400.21325932733
2.7695-3.17010.30211300.224226382768
3.1701-3.99330.25111240.199826762800
3.9933-39.07210.1921450.202828152960

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