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- PDB-3ljd: The X-ray structure of zebrafish RNase1 from a new crystal form a... -

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Basic information

Entry
Database: PDB / ID: 3ljd
TitleThe X-ray structure of zebrafish RNase1 from a new crystal form at pH 4.5
ComponentsZebrafish RNase1
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
ACETATE ION / Hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 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: Zebrafish RNase1
B: Zebrafish RNase1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,53411
Polymers28,7072
Non-polymers8289
Water7,368409
1
A: Zebrafish RNase1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7385
Polymers14,3531
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zebrafish RNase1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7976
Polymers14,3531
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Zebrafish RNase1
hetero molecules

B: Zebrafish RNase1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,53411
Polymers28,7072
Non-polymers8289
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+3/2,-y,z-1/21
Buried area1330 Å2
ΔGint-6 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.339, 48.971, 109.913
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 Zebrafish RNase1


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


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 293 K / pH: 4.5
Details: Drops were prepared by mixing equal volumes of protein solution (15 mg/ml) and reservoir solution (2M ammonium sulphate and 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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2008 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. obs: 41877 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AGI

1agi


Resolution: 1.38→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.182 4052 RANDOM
Rwork0.148 --
obs0.148 36128 -
all-40180 -
Refinement stepCycle: LAST / Resolution: 1.38→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 44 409 2453
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
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_deg
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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