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- PDB-1oj8: Novel and retro Binding Modes in Cytotoxic Ribonucleases from Ran... -

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Basic information

Entry
Database: PDB / ID: 1oj8
TitleNovel and retro Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with d(ApCpGpA) and (2',5'CpG)
Components
  • 5'-D(*AP*CP*GP*AP)-3'
  • RC-RNASE6 RIBONUCLEASE
KeywordsHYDROLASE / CYTOTOXIC RIBONUCLEASES / ANTI-TUMOR ACTIVITY / SIALIC BINDING AND NUCLEOTIDE BINDING
Function / homology
Function and homology information


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
DNA / RC-RNase6 ribonuclease
Similarity search - Component
Biological speciesRANA CATESBEIANA (American bullfrog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTsai, C.-J. / Liu, J.-H. / Liao, Y.-D. / Chen, L.-Y. / Cheng, P.-T. / Sun, Y.-J.
CitationJournal: To be Published
Title: Retro and Novel Binding Modes in Cytotoxic Ribonucleases from Rana Catesbeiana of Two Crystal Structures Complexed with (2',5'Cpg) and D(Apcpgpa)
Authors: Tsai, C.-J. / Liu, J.-H. / Liao, Y.-D. / Chen, L.-Y. / Cheng, P.-T. / Sun, Y.-J.
History
DepositionJul 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RC-RNASE6 RIBONUCLEASE
B: 5'-D(*AP*CP*GP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5774
Polymers13,3852
Non-polymers1922
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area839 Å2
ΔGint-24 kcal/mol
Surface area7370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.230, 61.230, 65.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21A-2089-

HOH

31A-2127-

HOH

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Components

#1: Protein RC-RNASE6 RIBONUCLEASE / RIBONUCLEASE


Mass: 12185.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) RANA CATESBEIANA (American bullfrog) / Tissue: OCCYTE / References: UniProt: Q9DFY5
#2: DNA chain 5'-D(*AP*CP*GP*AP)-3'


Mass: 1199.844 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.59 Å3/Da / Density % sol: 53 %
Crystal growpH: 7 / Details: 3.3 M AMMONIUM SULFATE,2% PEG 400, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 12965 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 7.32 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 35.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ONC

1onc


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1218 10.4 %RANDOM
Rwork0.229 ---
obs0.229 11741 82 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å20 Å2
2--3.45 Å20 Å2
3----6.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 83 10 220 1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 179 10.7 %
Rwork0.29 1491 -
obs--72.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PCA123.PARAMPROTEIN)PCA123.TOP
X-RAY DIFFRACTION2ACGA.PARAMACGA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP

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