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- PDB-1km9: The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana... -

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Basic information

Entry
Database: PDB / ID: 1km9
TitleThe Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog)
ComponentsRIBONUCLEASE, OOCYTES
KeywordsHYDROLASE / RC-RNase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / carbohydrate binding / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / extracellular region
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 / Oocytes ribonuclease
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsChern, S.-S. / Musayev, F.N. / Amiraslanov, I.R. / Liao, Y.-D. / Liaw, Y.-C.
Citation
Journal: To be Published
Title: The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog)
Authors: Chern, S.-S. / Musayev, F.N. / Amiraslanov, I.R. / Liao, Y.-D. / Liaw, Y.-C.
#1: Journal: J.Biomol.NMR / Year: 1996
Title: The Secondary Structure of a Pyrimidine-Guanine Sequence-Specific Ribonuclease Possessing Cytotoxic Activity From the Oocytes of Rana Catesbeiana
Authors: Chen, C. / Hom, K. / Huang, R.F. / Chou, P.J. / Liao, Y.D. / Huang, T.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: The Solution Structure of a Cytotoxic Ribonuclease From the Oocytes of Rana catesbeiana (bullfrog)
Authors: Chang, C.F. / Chen, C. / Chen, Y.C. / Hom, K. / F Huang, R. / Huang, T.H.
#3: Journal: J.Biol.Chem. / Year: 1998
Title: The Rana catesbeiana rcr gene encoding a cytotoxic ribonuclease : Tissue distribution, cloning, purification, cytotoxicity, and active residues for RNase activity
Authors: Huang, H.C. / Wang, S.C. / Leu, Y.J. / Lu, S.C. / Liao, Y.D.
#4: Journal: Nucleic Acids Res. / Year: 2000
Title: Purification and cloning of cytotoxic ribonucleases from Rana catesbeiana (bullfrog)
Authors: Liao, Y.D. / Huang, H.C. / Leu, Y.J. / Wei, C.W. / C Tang, P. / Wang, S.C.
History
DepositionDec 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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 16, 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_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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE, OOCYTES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7444
Polymers12,4591
Non-polymers2853
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.806, 45.918, 57.459
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 RIBONUCLEASE, OOCYTES / RC-RNASE


Mass: 12459.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: oocytes / Source: (natural) Rana catesbeiana (American bullfrog) / References: UniProt: P11916, EC: 3.1.27.5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 108 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium phosphate, NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 25, 1998 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→24.36 Å / Num. all: 8085 / Num. obs: 8085 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.62 % / Biso Wilson estimate: 17.7 Å2 / Limit h max: 20 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 29 / Limit l min: 0 / Observed criterion F max: 599537.23 / Observed criterion F min: 0.89 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 7.06 / Num. unique all: 402 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RCA

1rca


Resolution: 1.96→24.36 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 672 8.4 %RANDOM
Rwork0.178 ---
all0.181 8607 --
obs0.181 7970 92.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 47.953 Å2 / ksol: 0.309465 e/Å3
Displacement parametersBiso max: 85.72 Å2 / Biso mean: 29.53 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.82 Å20 Å20 Å2
2--10.91 Å20 Å2
3----4.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.12 Å
Luzzati d res high-1.96
Refinement stepCycle: LAST / Resolution: 1.96→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 15 108 987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_improper_angle_d1.22
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.96-2.050.301918.50.1988150.021107190684.6
2.05-2.150.276767.30.1998580.023103893490
2.15-2.290.313656.10.1839040.023105896991.6
2.29-2.460.238807.60.28890.023105396992
2.46-2.710.265807.40.2089270.0231076100793.6
2.71-3.10.26928.60.2079230.0221066101595.2
3.1-3.910.164827.50.169770.0181098105996.4
3.91-24.360.1731069.20.15210050.0151153111196.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5pca.parpca.top

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