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- PDB-3fd7: Crystal structure of Onconase C87A/C104A-ONC -

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Basic information

Entry
Database: PDB / ID: 3fd7
TitleCrystal structure of Onconase C87A/C104A-ONC
ComponentsProtein P-30
KeywordsHYDROLASE / Onconase / C-terminal disulfide bond / Endonuclease / Nuclease / Pyrrolidone carboxylic acid
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.531 Å
AuthorsNeumann, P. / Schulenburg, C. / Arnold, U. / Ulbrich-Hofmann, R. / Stubbs, M.T.
CitationJournal: Chembiochem / Year: 2010
Title: Impact of the C-terminal disulfide bond on the folding and stability of onconase.
Authors: Schulenburg, C. / Weininger, U. / Neumann, P. / Meiselbach, H. / Stubbs, M.T. / Sticht, H. / Balbach, J. / Ulbrich-Hofmann, R. / Arnold, U.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
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 2.1Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein P-30
B: Protein P-30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,57413
Polymers23,5632
Non-polymers1,01111
Water6,395355
1
A: Protein P-30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5089
Polymers11,7821
Non-polymers7278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein P-30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0664
Polymers11,7821
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-91 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.460, 51.190, 87.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein P-30 / Onconase


Mass: 11781.518 Da / Num. of mol.: 2 / Mutation: C87A, C104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / Plasmid: pET26b(+) / 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammoniumsulfate, 30% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2008 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→26.864 Å / Num. all: 31616 / Num. obs: 31390 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.35 % / Biso Wilson estimate: 21.64 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.074 / Net I/σ(I): 32.52
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 18.78 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 5.76 / Num. unique all: 4680 / Rsym value: 0.572 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.42 / Packing: 0
Highest resolutionLowest resolution
Rotation1.53 Å26.86 Å
Translation1.53 Å26.86 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ONC

1onc


Resolution: 1.531→26.864 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.898 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1571 5 %RANDOM
Rwork0.138 ---
obs0.14 31390 99.5 %-
all-31616 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.834 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 55.25 Å2 / Biso mean: 18.07 Å2 / Biso min: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.114 Å20 Å2-0 Å2
2--0.019 Å20 Å2
3----1.133 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.179 Å0.169 Å
Luzzati d res low-8 Å
Luzzati sigma a0.182 Å0.175 Å
Refinement stepCycle: LAST / Resolution: 1.531→26.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 57 355 2048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061797
X-RAY DIFFRACTIONf_angle_d1.162427
X-RAY DIFFRACTIONf_chiral_restr0.08268
X-RAY DIFFRACTIONf_plane_restr0.005301
X-RAY DIFFRACTIONf_dihedral_angle_d15.677653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.531-1.5810.2991340.212518265294
1.581-1.6370.2371420.14427042846100
1.637-1.7030.2261410.11926732814100
1.703-1.780.1891410.10826812822100
1.78-1.8740.1811410.10226912832100
1.874-1.9910.161420.10827002842100
1.991-2.1450.1851440.11327292873100
2.145-2.3610.1821430.12427132856100
2.361-2.7020.2021440.14227352879100
2.702-3.4030.1961460.13927792925100
3.403-26.8680.1431530.13328963049100

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