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- PDB-1oj1: Nonproductive and Novel Binding Modes in Cytotoxic Ribonucleases ... -

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Basic information

Entry
Database: PDB / ID: 1oj1
TitleNonproductive and Novel Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with (2,5 CpG) and d(ApCpGpA)
ComponentsRC-RNASE6 RIBONUCLEASE
KeywordsHYDROLASE / CYTOTOXIC RIBONUCLEASES / ANTI-TUMOR ACTIVITY / SIALIC BINDING AND NUCLEOTIDE BINDING
Function / homology
Function and homology information


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
CYTIDYL-2'-5'-PHOSPHO-GUANOSINE / RC-RNase6 ribonuclease
Similarity search - Component
Biological speciesRANA CATESBEIANA (American bullfrog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTsai, C.-J. / Liu, J.-H. / Liao, Y.-D. / Chen, L.-y. / Cheng, P.-T. / Sun, Y.-J.
CitationJournal: To be Published
Title: Nonproductive and Novel Binding Modes in Cytotoxic Ribonucleases from Rana Catesbeiana of Two Crystal Structures Complexed with C(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
DepositionJun 28, 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 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Other / Polymer sequence / Category: entity_poly / pdbx_database_status
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 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
A: RC-RNASE6 RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8703
Polymers12,1851
Non-polymers6842
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.800, 61.800, 65.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RC-RNASE6 RIBONUCLEASE


Mass: 12185.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) RANA CATESBEIANA (American bullfrog) / Organ: OOCYTES / References: UniProt: Q9DFY5
#2: Chemical ChemComp-CG2 / CYTIDYL-2'-5'-PHOSPHO-GUANOSINE


Mass: 588.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N8O12P
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.59 Å3/Da / Density % sol: 53 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRIE
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 53962 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 3.45 / % possible all: 98.2

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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: 2.1→20 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 722 10.6 %RANDOM
Rwork0.203 ---
obs0.203 6785 86.3 %-
Solvent computationSolvent model: FLAT / Bsol: 67.3609 Å2 / ksol: 0.39614 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.62 Å20 Å20 Å2
2--5.62 Å20 Å2
3---11.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 45 107 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.3
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_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 102 11.3 %
Rwork0.209 804 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CPG_NOH.PARAMCPG_NOH.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP

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