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- PDB-1ahb: THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMP... -

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Basic information

Entry
Database: PDB / ID: 1ahb
TitleTHE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN
ComponentsALPHA-MOMORCHARIN
KeywordsGLYCOSIDASE
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
FORMYCIN-5'-MONOPHOSPHATE / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsRen, J. / Wang, Y. / Dong, Y. / Stuart, D.I.
Citation
Journal: Structure / Year: 1994
Title: The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin.
Authors: Ren, J. / Wang, Y. / Dong, Y. / Stuart, D.I.
#1: Journal: Daresbury Lab.[Rep.]Dl/Sci/R / Year: 1992
Title: Molecular Replacement Studies of Alpha-Momorcharin (in: Proceedings of the Ccp4 Study Weekend: Molecular Replacement, Edited by E.J.Dodson, S.Gover,W.Wolf)
Authors: Ren, J. / Wang, Y. / Dong, Y. / Stuart, D.I.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystals of Alpha-Momorcharin, a New Ribosome-Inactivating Protein
Authors: Feng, Z. / Li, W.W. / Yeung, H.W. / Chen, S. / Wang, Y. / Lin, X. / Dong, Y. / Wang, J.
History
DepositionJan 7, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: ALPHA-MOMORCHARIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7442
Polymers27,3961
Non-polymers3471
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.400, 131.400, 49.800
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 ALPHA-MOMORCHARIN


Mass: 27396.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Chemical ChemComp-FMP / FORMYCIN-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal grow
*PLUS
pH: 7.65 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(w/v)1drop(NH4)2SO4
20.05 MTris-HCl1drop
34 %(w/v)protein1drop
423 %(w/v)1reservoir(NH4)2SO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 100 Å / Num. obs: 10409 / % possible obs: 85.8 % / Observed criterion σ(I): 3 / Num. measured all: 11153 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / % possible obs: 59.3 % / Num. unique obs: 2018 / Num. measured obs: 2453 / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.175 / Rfactor obs: 0.175 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 23 80 2036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.175 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.89

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