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- PDB-2pqi: Crystal structure of active ribosome inactivating protein from ma... -

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Basic information

Entry
Database: PDB / ID: 2pqi
TitleCrystal structure of active ribosome inactivating protein from maize (b-32)
ComponentsRibosome-inactivating protein 3
KeywordsHYDROLASE / MOD / ribosome inactivating protein / maize / Plant defense / Protein synthesis inhibitor / Toxin
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation / cytoplasm
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
Ribosome-inactivating protein 3 / Ribosome-inactivating protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMak, A.N.S. / Wong, Y.T. / Young, J.A. / Cha, S.S. / Sze, K.H. / Au, S.W.N. / Wong, K.B. / Shaw, P.C.
Citation
Journal: Nucleic Acids Res. / Year: 2007
Title: Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site.
Authors: Mak, A.N. / Wong, Y.T. / An, Y.J. / Cha, S.S. / Sze, K.H. / Au, S.W. / Wong, K.B. / Shaw, P.C.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Characterization and molecular cloning of a proenzyme form of a ribosome-inactivating protein from maize. Novel mechanism of proenzyme activation by proteolytic removal of a 2.8-kilodalton ...Title: Characterization and molecular cloning of a proenzyme form of a ribosome-inactivating protein from maize. Novel mechanism of proenzyme activation by proteolytic removal of a 2.8-kilodalton internal peptide segment.
Authors: Walsh, T.A. / Morgan, A.E. / Hey, T.D.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-inactivating protein 3
B: Ribosome-inactivating protein 3
C: Ribosome-inactivating protein 3


Theoretical massNumber of molelcules
Total (without water)81,9173
Polymers81,9173
Non-polymers00
Water1,56787
1
A: Ribosome-inactivating protein 3


Theoretical massNumber of molelcules
Total (without water)27,3061
Polymers27,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome-inactivating protein 3


Theoretical massNumber of molelcules
Total (without water)27,3061
Polymers27,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribosome-inactivating protein 3


Theoretical massNumber of molelcules
Total (without water)27,3061
Polymers27,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.190, 115.190, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Ribosome-inactivating protein 3 / rRNA N-glycosidase / B-32 protein


Mass: 27305.551 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: b-32, CRIP3 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: P25891, UniProt: P28522*PLUS, rRNA N-glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium acetate tri-hydrate, 0.1 M Tris-HCl pH 8.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 21654 / Num. obs: 21654 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 22.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.1 / % possible all: 90.1

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PQG

2pqg


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1115 -Random
Rwork0.2172 ---
all0.2172 20539 --
obs0.2172 20539 93.9 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5409 0 0 87 5496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00795
X-RAY DIFFRACTIONc_angle_deg1.4491

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