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- PDB-4o8e: Crystal structure of the complex of type I ribosome inactivating ... -

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Basic information

Entry
Database: PDB / ID: 4o8e
TitleCrystal structure of the complex of type I ribosome inactivating protein from Momordica balsamina with uridine triphosphate at 2.0 A resolution
ComponentsrRNA N-glycosidaseRRNA N-glycosylase
KeywordsHYDROLASE / Ligand binding / uridine diphosphate / uridine triphosphate
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / nucleotide binding
Similarity search - Function
Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein / Ribosome inactivating protein ...Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein / Ribosome inactivating protein / Ribosome-inactivating protein superfamily / Ribosome-inactivating protein, subdomain 2 / Irregular / Few Secondary Structures / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / rRNA N-glycosidase
Similarity search - Component
Biological speciesMomordica balsamina (balsam apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPandey, S. / Yamini, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of type I ribosome inactivating protein from Momordica balsamina with uridine triphosphate at 2.0 A resolution
Authors: Pandey, S. / Yamini, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rRNA N-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9835
Polymers27,0941
Non-polymers8904
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.014, 130.014, 40.043
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein rRNA N-glycosidase / RRNA N-glycosylase


Mass: 27093.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica balsamina (balsam apple) / References: UniProt: D9J2T9, rRNA N-glycosylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2013 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16200 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.065 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.364 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S9Q
Resolution: 2→37.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.046 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21228 865 5.1 %RANDOM
Rwork0.17174 ---
all0.17375 16200 --
obs0.17375 16200 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.698 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-1 Å2-0 Å2
2---1 Å20 Å2
3---3.24 Å2
Refinement stepCycle: LAST / Resolution: 2→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 55 223 2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192002
X-RAY DIFFRACTIONr_bond_other_d0.0020.021914
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9972730
X-RAY DIFFRACTIONr_angle_other_deg0.71134381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60223.92984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63615322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3561513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_mcbond_it1.0182.969983
X-RAY DIFFRACTIONr_mcbond_other1.0172.967982
X-RAY DIFFRACTIONr_mcangle_it1.7494.4461227
X-RAY DIFFRACTIONr_mcangle_other1.7494.4481228
X-RAY DIFFRACTIONr_scbond_it1.2923.2981019
X-RAY DIFFRACTIONr_scbond_other1.2543.2371007
X-RAY DIFFRACTIONr_scangle_other2.144.7861484
X-RAY DIFFRACTIONr_long_range_B_refined6.70825.8272453
X-RAY DIFFRACTIONr_long_range_B_other6.71125.752450
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 66 -
Rwork0.228 1156 -
obs--98.23 %

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