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- PDB-3ln8: The X-ray structure of Zf-RNase-1 from a new crystal form at pH 7.3 -

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Basic information

Entry
Database: PDB / ID: 3ln8
TitleThe X-ray structure of Zf-RNase-1 from a new crystal form at pH 7.3
ComponentsHYDROLASE
KeywordsHYDROLASE / angiogenins / fish rnases
Function / homology
Function and homology information


endonuclease activity / nucleic acid binding
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
Biological speciesDanio Rerio (zebrafish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsRusso Krauss, I. / Merlino, A. / 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: 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.
#2: Journal: Gene / Year: 2007
Title: The success of the RNase scaffold in the advance of biosciences and in evolution
Authors: Pizzo, E. / D'Alessio, G.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 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_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: HYDROLASE
B: HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,66712
Polymers28,7072
Non-polymers96110
Water6,864381
1
A: HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8346
Polymers14,3531
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8346
Polymers14,3531
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: HYDROLASE
hetero molecules

B: HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,66712
Polymers28,7072
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+3/2,-y,z-1/21
Buried area1360 Å2
ΔGint-5 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.573, 49.183, 110.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYDROLASE /


Mass: 14353.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio Rerio (zebrafish) / Production host: Escherichia coli (E. coli) / References: UniProt: E7FH76*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 1.96 Å3/Da / Density % sol: 37.36 %
Crystal growTemperature: 293 K / pH: 7.3
Details: 2.0 M ammonium sulphate, 0.1 M TRIS/acetate, pH 7.3, 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: Jun 9, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→30 Å / Num. obs: 28093 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.61→1.67 Å / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LJD

3ljd


Resolution: 1.61→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2723 -RANDOM
Rwork0.146 ---
obs0.146 27488 91 %-
Refinement stepCycle: LAST / Resolution: 1.61→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 50 381 2436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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