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- PDB-5cf9: Cleavage of nicotinamide adenine dinucleotide by the ribosome ina... -

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Basic information

Entry
Database: PDB / ID: 5cf9
TitleCleavage of nicotinamide adenine dinucleotide by the ribosome inactivating protein of Momordica charantia - enzyme-NADP+ co-crystallisation.
ComponentsRibosome-inactivating protein momordin I
KeywordsHYDROLASE / Product / complex / glycosidase / NADP
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / 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 / 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 ...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. / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsVinkovic, M. / Wood, S.P. / Gill, R. / Husain, J. / Wood, G.E. / Dunn, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Cleavage of nicotinamide adenine dinucleotide by the ribosome-inactivating protein from Momordica charantia.
Authors: Vinkovic, M. / Dunn, G. / Wood, G.E. / Husain, J. / Wood, S.P. / Gill, R.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
B: Ribosome-inactivating protein momordin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7403
Polymers27,3961
Non-polymers3432
Water3,639202
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint8 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.510, 130.510, 37.980
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 Ribosome-inactivating protein momordin I / Alpha-momorcharin / Alpha-MMC / rRNA N-glycosidase


Mass: 27396.285 Da / Num. of mol.: 1 / Fragment: residues 24-269 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / 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
#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.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: PEG 4000, sodium phosphate / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.917 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.52→62.5 Å / Num. all: 37103 / Num. obs: 37103 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.3
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2759 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOM

1mom


Resolution: 1.52→37.675 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 1830 4.93 %
Rwork0.1383 --
obs0.1398 37096 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→37.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 23 202 2157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082004
X-RAY DIFFRACTIONf_angle_d1.12723
X-RAY DIFFRACTIONf_dihedral_angle_d13.553739
X-RAY DIFFRACTIONf_chiral_restr0.042316
X-RAY DIFFRACTIONf_plane_restr0.006351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.56110.32421240.2382756X-RAY DIFFRACTION100
1.5611-1.60710.26911380.21332662X-RAY DIFFRACTION100
1.6071-1.6590.25571520.18532731X-RAY DIFFRACTION100
1.659-1.71830.23711360.16382702X-RAY DIFFRACTION100
1.7183-1.7870.21381290.14922717X-RAY DIFFRACTION100
1.787-1.86840.20221580.13362708X-RAY DIFFRACTION100
1.8684-1.96690.17421500.11942711X-RAY DIFFRACTION100
1.9669-2.09010.18321330.11592707X-RAY DIFFRACTION100
2.0901-2.25150.1511270.11532738X-RAY DIFFRACTION100
2.2515-2.4780.14521240.1212743X-RAY DIFFRACTION100
2.478-2.83650.16261570.12862694X-RAY DIFFRACTION100
2.8365-3.57320.16191330.13522702X-RAY DIFFRACTION100
3.5732-37.68660.151690.14632695X-RAY DIFFRACTION100

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