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- PDB-3u00: Crystal structure of wild-type onconase at 1.65 A resolution -

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Basic information

Entry
Database: PDB / ID: 3u00
TitleCrystal structure of wild-type onconase at 1.65 A resolution
ComponentsProtein P-30
KeywordsHYDROLASE / ANTITUMOR PROTEIN / alpha/beta protein / ranpirnase / endonuclease / nuclease
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium
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
PHOSPHATE ION / Protein P-30
Similarity search - Component
Biological speciesRana pipiens (northern leopard frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsKurpiewska, K. / Torrent, G. / Ribo, M. / Vilanova, M. / Loch, J. / Lewinski, K.
CitationJournal: To be Published
Title: Crystal structure of wild-type onconase at 1.65 A resolution
Authors: Kurpiewska, K. / Torrent, G. / Ribo, M. / Vilanova, M. / Loch, J. / Lewinski, K.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag / _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: Protein P-30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3216
Polymers11,8461
Non-polymers4755
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.509, 39.454, 69.985
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 Protein P-30 / Onconase


Mass: 11845.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / Plasmid: PET22B(+)/PONC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.89 Å3/Da / Density % sol: 35.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% w/v PEG8000, 0.05 M potassium phosphate monobasic, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→15.029 Å / Num. all: 11323 / Num. obs: 11256 / % possible obs: 93.8 % / Redundancy: 2.7 % / Rsym value: 0.09 / Net I/σ(I): 5.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.97 / Model details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrysalisProdata collection
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ONC

1onc


Resolution: 1.65→15.029 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.248 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1197 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1127 10 %RANDOM
Rwork0.17117 ---
obs0.17661 10129 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.756 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 25 97 948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9761270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84324.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96215167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.116153
X-RAY DIFFRACTIONr_chiral_restr0.1460.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021677
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.5555
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.872922
X-RAY DIFFRACTIONr_scbond_it3.1873371
X-RAY DIFFRACTIONr_scangle_it5.0334.5343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 85 -
Rwork0.276 721 -
obs--100 %

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