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- PDB-3mvg: Native structure of IRIP, a type I ribosome inactivating protein ... -

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Basic information

Entry
Database: PDB / ID: 3mvg
TitleNative structure of IRIP, a type I ribosome inactivating protein from Iris hollandica var. at 1.25 A
ComponentsRibosome inactivating type 1 protein
KeywordsHYDROLASE / Ribosome inactivating protein type I / IRIP / Pi-Loop
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 type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein ...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 / 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
Biological speciesIris hollandica (Dutch iris)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMeyer, A. / Weber, W. / Singh, T.P. / Betzel, C.
Citation
Journal: to be published
Title: Native structure of IRIP, a type I ribosome inactivating protein from Iris hollandica var. at 1.25 A
Authors: Meyer, A. / Weber, W. / Singh, T.P. / Betzel, C.
#1: Journal: Biochem.J. / Year: 1997
Title: Type 1 ribosome-inactivating proteins are the most abundant proteins in iris (Iris hollandica var. Professor Blaauw) bulbs: characterization and molecular cloning
Authors: Van Damme, E.J. / Barre, A. / Barbieri, L. / Valbonesi, P. / Rouge, P. / Van Leuven, F. / Stirpe, F. / Peumans, W.J.
#2: Journal: Protein Eng. / Year: 1992
Title: Analysis of several key active site residues of ricin A chain by mutagenesis and X-ray crystallography
Authors: Kim, Y. / Robertus, J.D.
#3: Journal: Proteins / Year: 1991
Title: Site-directed mutagenesis of ricin A-chain and implications for the mechanism of action
Authors: Ready, M.P. / Kim, Y. / Robertus, J.D.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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: Ribosome inactivating type 1 protein
B: Ribosome inactivating type 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,89821
Polymers62,1282
Non-polymers1,77019
Water13,619756
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.879, 84.809, 69.080
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE IRIP DIMER IN THE ASYMMETRIC UNIT HAS BEEN FOUND IN AN NON-CRYSTALLOGRAPHIC 2-FOLD SYMMETRY. FORMATION OF THAT DIMER HAS PROBABLY NO BIOLOGICAL MEANING AND IS A RESULT OF THE CRYSTALLIZATION PROCESS.

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Components

#1: Protein Ribosome inactivating type 1 protein / IRIP


Mass: 31064.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Iris hollandica (Dutch iris) / References: UniProt: O04358, rRNA N-glycosylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE CONFLICTS BETWEEN THE SEQUENCE AND DATABASE REFERENCE SEQUENCE. THE RESIDUES ARE ...THERE ARE CONFLICTS BETWEEN THE SEQUENCE AND DATABASE REFERENCE SEQUENCE. THE RESIDUES ARE CONSISTENT WITH ELECTRON DENSITY. FOR THR A 134, B 105 AND B 134, THEY ARE REFERRED IN BIOCHEM J. 1997 JUN 15;324 (PT 3):963-70; VAN DAMME EJ ET AL.

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.9M ammonium sulfate in 20% w/v glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 157596 / % possible obs: 99.8 % / Observed criterion σ(I): 2.6 / Redundancy: 4.4 % / Biso Wilson estimate: 17.62 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.447 / Net I/σ(I): 25.6 / Num. measured all: 1839695
Reflection shellResolution: 1.247→1.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.67 / Num. unique all: 7666 / Rsym value: 0.45 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2T

1m2t


Resolution: 1.25→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.646 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Ala 93 (A/B) and Glycin 251 were refined based on the electron density results. Results are discussed in the publication.
RfactorNum. reflection% reflectionSelection details
Rfree0.18542 7893 5 %RANDOM
Rwork0.16846 ---
obs0.16931 157596 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.71 Å2
2---0.11 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 109 756 4855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224543
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.976221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80522.891211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45515735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3311551
X-RAY DIFFRACTIONr_chiral_restr0.0780.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213471
X-RAY DIFFRACTIONr_mcbond_it0.521.52736
X-RAY DIFFRACTIONr_mcangle_it0.98724528
X-RAY DIFFRACTIONr_scbond_it1.4731807
X-RAY DIFFRACTIONr_scangle_it2.3074.51693
LS refinement shellResolution: 1.247→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 559 -
Rwork0.251 10550 -
obs--95.31 %

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