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- PDB-1dix: CRYSTAL STRUCTURE OF RNASE LE -

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Basic information

Entry
Database: PDB / ID: 1dix
TitleCRYSTAL STRUCTURE OF RNASE LE
ComponentsEXTRACELLULAR RIBONUCLEASE LE
KeywordsHYDROLASE / ALPHA PLUS BETA
Function / homology
Function and homology information


ribonuclease T2 / ribonuclease T2 activity / RNA catabolic process / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
Ribonuclease T2, eukaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily ...Ribonuclease T2, eukaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Extracellular ribonuclease LE
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.65 Å
AuthorsTanaka, N. / Nakamura, K.T.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a plant ribonuclease, RNase LE.
Authors: Tanaka, N. / Arai, J. / Inokuchi, N. / Koyama, T. / Ohgi, K. / Irie, M. / Nakamura, K.T.
#1: Journal: Protein Pept.Lett. / Year: 1999
Title: Crystallization and Preliminary X-ray Crystallographic Studies of Ribonuclease LE from Lycopersicon esculentum
Authors: Tanaka, N. / Arai, J. / Inokuchi, N. / Koyama, T. / Ohgi, K. / Irie, M. / Nakamura, K.T.
History
DepositionNov 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: EXTRACELLULAR RIBONUCLEASE LE


Theoretical massNumber of molelcules
Total (without water)22,9121
Polymers22,9121
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.02, 78.79, 32.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EXTRACELLULAR RIBONUCLEASE LE


Mass: 22912.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P80022, EC: 3.1.27.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG1540, CITRATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMcitrate1drop
336 %(w/v)PEG15401reservoir
40.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. all: 144121 / Num. obs: 22385 / % possible obs: 93.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.049
Reflection
*PLUS
Num. measured all: 144121 / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.65→40 Å / σ(F): 1 /
RfactorNum. reflection
Rfree0.278 -
Rwork0.219 -
obs-22353
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 0 136 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_planar_d0.0440.05
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 1 / Num. reflection Rfree: 2296 / % reflection Rfree: 10 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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