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- PDB-1m07: RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTO... -

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Basic information

Entry
Database: PDB / ID: 1m07
TitleRESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA)
Components
  • 5'-D(*AP*CP*GP*A)-3'
  • Ribonuclease
KeywordsHYDROLASE/DNA / RC-RNase-d(ACGA) / ribonuclease / bullfrog / cytotoxicity / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / carbohydrate binding / angiogenesis / endonuclease activity / defense response to Gram-negative bacterium / 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
DNA / Oocytes ribonuclease
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeu, Y.-J. / Chern, S.-S. / Wang, S.-C. / Hsiao, Y.-Y. / Amiraslanov, I. / Liaw, Y.-C. / Liao, Y.-D.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography
Authors: Leu, Y.-J. / Chern, S.-S. / Wang, S.-C. / Hsiao, Y.-Y. / Amiraslanov, I. / Liaw, Y.-C. / Liao, Y.-D.
#1: Journal: To be Published
Title: THE CRYSTAL STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA
Authors: Leu, Y.-J. / Chern, S.-S. / Wang, S.-C. / Hsiao, Y.-Y. / Amiraslanov, I.R. / Liaw, Y.-C. / Liao, Y.-D.
#2: Journal: J.BIOMOL.NMR / Year: 1996
Title: THE SECONDARY STRUCTURE OF A PYRIMIDINE-GUANINE SEQUENCE-SPECIFIC RIBONUCLEASE POSSESSING CYTOTOXIC ACTIVITY FROM THE OOCYTE OF RANA CATESBEIANA
Authors: Chen, C. / Hom, K. / Huang, R.F. / Chou, P.J. / Liao, Y.D. / Huang, T.
#3: Journal: J.Mol.Biol. / Year: 1998
Title: THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA (BULLFROG)
Authors: Chang, C.F. / Chen, C. / Chen, Y.C. / Hom, K. / Huang, R.F. / Huang, T.H.
#4: 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.
#5: Journal: Nucleic Acids Res. / Year: 2000
Title: PURIFICATION AND CLONING OF CYTOTOXIC RIBONUCLEASE FROM RANA CATESBEIANA (BULLFROG)
Authors: Liao, Y.D. / Huang, H.C. / Leu, Y.J. / Wei, C.W. / Tang, P.C. / Wang, S.C.
History
DepositionJun 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Other
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
Remark 400COMPOUND THE ATOMS (C6, N9, C4, C4', C5', C2', N7, C8, N1) OF RESIDUE 4 CHAIN C,D WAS FIXED IN THE REFINEMENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*CP*GP*A)-3'
D: 5'-D(*AP*CP*GP*A)-3'
A: Ribonuclease
B: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)27,3184
Polymers27,3184
Non-polymers00
Water5,819323
1
C: 5'-D(*AP*CP*GP*A)-3'
A: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)13,6592
Polymers13,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*AP*CP*GP*A)-3'
B: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)13,6592
Polymers13,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.629, 53.566, 72.203
Angle α, β, γ (deg.)90.00, 98.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*AP*CP*GP*A)-3'


Mass: 1199.844 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Ribonuclease / RC-RNase / Sialic acid-binding lectin / SBL-C


Mass: 12459.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rana catesbeiana (American bullfrog) / Organ: oocytes / References: UniProt: P11916, EC: 3.1.27.5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.02 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
24 mMTris-HCl1droppH8.0
34 mM1dropNaCl
40.1 Mpotassium/sodium tartrate tetrahydrate1reservoir
524 %(w/v)PEG80001reservoir
60.05 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2000 / Details: KOHZU double crystal monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.79→19.68 Å / Num. all: 20226 / Num. obs: 18075 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.81 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.2 / Num. unique all: 894 / Rsym value: 0.18 / % possible all: 90.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 20226 / Num. measured all: 137742
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassificationNB
CNS1refinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KM8

1km8


Resolution: 1.8→19.68 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1369 7.8 %RANDOM
Rwork0.189 ---
all0.227 20134 --
obs0.227 17518 87 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 68.8524 Å2 / ksol: 0.437359 e/Å3
Displacement parametersBiso mean: 25.29 Å2
Baniso -1Baniso -2Baniso -3
1-15.03 Å20 Å22.85 Å2
2---7.76 Å20 Å2
3----7.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 160 0 323 2219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_torsion_deg26.4
X-RAY DIFFRACTIONx_torsion_impr_deg4.3
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_improper_angle_d4.3
X-RAY DIFFRACTIONx_mcbond_it1.271.5
X-RAY DIFFRACTIONx_mcangle_it1.842
X-RAY DIFFRACTIONx_scbond_it2.092
X-RAY DIFFRACTIONx_scangle_it3.142.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
1.8-1.880.27141636.60.24318800.01982.3
1.88-1.980.28711566.20.23219570.01984
1.98-2.10.27071676.70.21719360.01784.1
2.1-2.270.25071676.70.19419380.01584.1
2.27-2.50.239717670.18719480.01484.8
2.5-2.860.2621666.50.19421300.01590.1
2.86-3.590.2117870.16822030.01394.1
3.59-19.680.19011967.60.17521570.01391.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5pca.parampca.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.3
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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