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- PDB-7mlt: Crystal structure of ricin A chain in complex with 5-(2-ethylphen... -

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Basic information

Entry
Database: PDB / ID: 7mlt
TitleCrystal structure of ricin A chain in complex with 5-(2-ethylphenyl)thiophene-2-carboxylic acid
ComponentsRicin
KeywordsHydrolase/Hydrolase Inhibitor / Ricin chain-A / RTA / Hydrolase / Toxin / Inhibitor / 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
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 ...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
Similarity search - Domain/homology
5-(2-ethylphenyl)thiophene-2-carboxylic acid / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHarijan, R.K. / Li, X.P. / Cao, B. / Augeri, D. / Bonanno, J.B. / Almo, S.C. / Tumer, N.E. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072425 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design.
Authors: Li, X.P. / Harijan, R.K. / Cao, B. / Kahn, J.N. / Pierce, M. / Tsymbal, A.M. / Roberge, J.Y. / Augeri, D. / Tumer, N.E.
History
DepositionApr 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)31,52423
Polymers30,0681
Non-polymers1,45622
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.618, 168.618, 54.949
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-670-

HOH

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Components

#1: Protein Ricin /


Mass: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZJD / 5-(2-ethylphenyl)thiophene-2-carboxylic acid


Mass: 232.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.7 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM Magnesium Chloride, 16 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→84.45 Å / Num. obs: 43070 / % possible obs: 100 % / Redundancy: 21.8 % / CC1/2: 0.99 / Rpim(I) all: 0.03 / Net I/σ(I): 20.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 22.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2519 / CC1/2: 0.68 / Rpim(I) all: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC

1rtc


Resolution: 1.8→84.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.123 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 2193 5.1 %RANDOM
Rwork0.1772 ---
obs0.1785 40857 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.55 Å2 / Biso mean: 29.193 Å2 / Biso min: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.17 Å20 Å2
2---0.35 Å20 Å2
3---1.13 Å2
Refinement stepCycle: final / Resolution: 1.8→84.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 91 272 2388
Biso mean--48.92 44.29 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171993
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6742906
X-RAY DIFFRACTIONr_angle_other_deg1.3151.5684584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98820.945127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18615330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7071521
X-RAY DIFFRACTIONr_chiral_restr0.0660.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 170 -
Rwork0.278 2977 -
all-3147 -
obs--99.97 %

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