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- PDB-1onc: THE REFINED 1.7 ANGSTROMS X-RAY CRYSTALLOGRAPHIC STRUCTURE OF P-3... -

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Basic information

Entry
Database: PDB / ID: 1onc
TitleTHE REFINED 1.7 ANGSTROMS X-RAY CRYSTALLOGRAPHIC STRUCTURE OF P-30, AN AMPHIBIAN RIBONUCLEASE WITH ANTI-TUMOR ACTIVITY
ComponentsP-30 PROTEIN
KeywordsPANCREATIC RIBONUCLEASE
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
Biological speciesRana pipiens (northern leopard frog)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsMosimann, S.C. / Ardelt, W. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Refined 1.7 A X-ray crystallographic structure of P-30 protein, an amphibian ribonuclease with anti-tumor activity.
Authors: Mosimann, S.C. / Ardelt, W. / James, M.N.
#1: Journal: Proteins / Year: 1992
Title: Comparative Molecular Modeling and Crystallization of P-30 Protein: A Novel Anti-Tumor Protein of Rana Pipiens Oocytes and Early Embryos
Authors: Mosimann, S.C. / Johns, K.L. / Ardelt, W. / Mikulski, S.M. / Shogen, K. / James, M.N.G.
History
DepositionAug 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P-30 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9422
Polymers11,8461
Non-polymers961
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.530, 69.640, 32.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE N-TERMINAL RESIDUE (PCA 1) IS A PYROGLUTAMYL RESIDUE.

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Components

#1: Protein P-30 PROTEIN


Mass: 11845.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / References: UniProt: P22069
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
225 %satammonium sulfate1drop
35 mMacetate1drop
450 %satammonium sulfate1reservoir
510 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 9495 / % possible obs: 89.4 % / Num. measured all: 43858 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Mean I/σ(I) obs: 11

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.178 / Rfactor obs: 0.178 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 5 97 928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 8653 / σ(I): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d0.9
X-RAY DIFFRACTIONx_planar_d0.030.034
X-RAY DIFFRACTIONx_plane_restr0.010.009
X-RAY DIFFRACTIONx_chiral_restr0.20.216

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