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- PDB-2i5s: Crystal structure of onconase with bound nucleic acid -

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Basic information

Entry
Database: PDB / ID: 2i5s
TitleCrystal structure of onconase with bound nucleic acid
Components
  • 5'-D(*A*(DU)P*GP*A)-3'
  • P-30 protein
KeywordsHYDROLASE/DNA / Onconase / P-30 protein / ribonuclease / anti-tumor / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / 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 speciesRana pipiens (northern leopard frog)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBae, E. / Lee, J.E. / Raines, R.T. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis for catalysis by onconase.
Authors: Lee, J.E. / Bae, E. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T.
History
DepositionAug 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 25, 2018Group: Data collection
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source
Item: _diffrn_detector.type
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: P-30 protein
A: 5'-D(*A*(DU)P*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)13,0462
Polymers13,0462
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.229, 26.101, 32.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-252-

HOH

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Components

#1: Protein P-30 protein / 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) / Gene: RNP30_RANPI / Plasmid: pET 22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: DNA chain 5'-D(*A*(DU)P*GP*A)-3'


Mass: 1200.829 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.9 Å3/Da / Density % sol: 41.186596 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.003 M SINGLE-STRANDED DNA OLIGOMER) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (25% PEG 3350, 0.1 M HEPES PH 7.5) CRYO-PROTECTED WITH WELL SOLUTION ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.003 M SINGLE-STRANDED DNA OLIGOMER) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (25% PEG 3350, 0.1 M HEPES PH 7.5) CRYO-PROTECTED WITH WELL SOLUTION SUPPLEMENTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Hepes11
3ethylene glycol11
4HOH11
5PEG 335012
6Hepes12
7ethylene glycol12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 2, 2006 / Details: MONTEL OPTICS
RadiationMonochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→64.6145 Å / Num. obs: 9270 / % possible obs: 99.7 % / Redundancy: 9.84 % / Rmerge(I) obs: 0.1249 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
1.9-1.953.320.51722.5262495.9
1.95-24.420.45973.26634100
2-2.054.530.35453.97556100
2.05-2.154.730.31934.38936100
2.15-2.255.130.29845.15797100
2.25-2.355.990.26376.7696100
2.35-2.456.980.26227.43562100
2.45-2.557.920.2478.31471100
2.55-2.79.650.230810.22615100
2.7-2.8511.20.206312.58471100
2.85-3.0512.60.175214.74509100
3.05-3.315.090.145519.26490100
3.3-3.6518.540.115527.01471100
3.65-4.2520.650.089931.14497100
4.25-5.4521.130.076332.72471100
5.45-64.614520.550.079530.8447099.8

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Phasing

Phasing MRRfactor: 0.569 / Cor.coef. Fo:Fc: 0.23
Highest resolutionLowest resolution
Rotation3 Å32.49 Å
Translation3 Å32.49 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
SAINTdata reduction
RefinementStarting model: PDB ENTRY 1ONC

1onc


Resolution: 1.9→32.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.165 / SU B: 3.248 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 441 4.778 %RANDOM
Rwork0.178 ---
all0.181 ---
obs0.181 9229 99.719 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.207 Å20 Å20 Å2
2---0.009 Å20 Å2
3---0.216 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 41 0 155 1022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022893
X-RAY DIFFRACTIONr_angle_refined_deg1.4152.0081218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53324.57135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18315153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.535153
X-RAY DIFFRACTIONr_chiral_restr0.0980.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02642
X-RAY DIFFRACTIONr_nbd_refined0.20.2410
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.220
X-RAY DIFFRACTIONr_mcbond_it1.3612536
X-RAY DIFFRACTIONr_mcangle_it2.2094858
X-RAY DIFFRACTIONr_scbond_it4.1736417
X-RAY DIFFRACTIONr_scangle_it5.998360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.343260.20859164395.956
1.949-2.0030.262370.186632669100
2.003-2.0610.29290.178592621100
2.061-2.1240.237300.18585615100
2.124-2.1940.235300.188597627100
2.194-2.2710.246210.174520541100
2.271-2.3560.241400.178537577100
2.356-2.4520.348200.176521541100
2.452-2.5610.289240.179491515100
2.561-2.6860.199190.172477496100
2.686-2.8310.272190.175458477100
2.831-3.0020.281200.164438458100
3.002-3.2090.223260.17411437100
3.209-3.4660.157210.163373394100
3.466-3.7950.203170.162361378100
3.795-4.2420.243110.15329340100
4.242-4.8940.196180.16279297100
4.894-5.9860.274190.207254273100
5.986-8.4290.3570.245218225100
8.429-64.550.13670.262124131100

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