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- PDB-3lje: The X-ray structure of zebrafish RNase5 -

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Basic information

Entry
Database: PDB / ID: 3lje
TitleThe X-ray structure of zebrafish RNase5
ComponentsZebrafish RNase5
KeywordsHYDROLASE / angiogenins / fish rnases
Function / homology
Function and homology information


endonuclease activity / nucleic acid binding / hydrolase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Zebrafish RNase5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRusso Krauss, I. / Merlino, A. / Coscia, F. / Mazzarella, L. / Sica, F.
Citation
Journal: Biochem.J. / Year: 2010
Title: A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.
Authors: Pizzo, E. / Merlino, A. / Turano, M. / Russo Krauss, I. / Coscia, F. / Zanfardino, A. / Varcamonti, M. / Furia, A. / Giancola, C. / Mazzarella, L. / Sica, F. / D'Alessio, G.
#1: Journal: Gene / Year: 2007
Title: The success of the RNase scaffold in the advance of bioscience and in evolution.
Authors: Pizzo, E. / D'Alessio, G.
#2: Journal: J.Biol.Chem. / Year: 2006
Title: Ribonucleases and angiogenins from fish
Authors: Pizzo, E. / Buonanno, P. / Di Maro, A. / Ponticelli, S. / De Falco, S. / Quarto, N. / Cubellis, M.V. / D'Alessio, G.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zebrafish RNase5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7854
Polymers14,5341
Non-polymers2513
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.489, 126.489, 126.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Zebrafish RNase5


Mass: 14533.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Plasmid: PET22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: E7FH77*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 32% MPEG 2K, 0.2M ammonium sulfate, 0.1M sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 27, 2009 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16327 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LJD

3ljd


Resolution: 1.8→24.81 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.2 -RANDOM
Rwork0.169 --
obs0.169 13153 -
all-31245 -
Refinement stepCycle: LAST / Resolution: 1.8→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 14 110 1069

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