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- PDB-5et4: Structure of RNase A-K7H/R10H in complex with 3'-CMP -

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Basic information

Entry
Database: PDB / ID: 5et4
TitleStructure of RNase A-K7H/R10H in complex with 3'-CMP
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase A / p2 subsite / exonuclease activity
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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
CYTIDINE-3'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBlanco, J.A. / Salazar, V.A. / Moussaoui, M. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spain
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates.
Authors: Prats-Ejarque, G. / Blanco, J.A. / Salazar, V.A. / Nogues, V.M. / Moussaoui, M. / Boix, E.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.4Jan 10, 2024Group: 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
Revision 1.5Nov 13, 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 pancreatic
B: Ribonuclease pancreatic
C: Ribonuclease pancreatic
D: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2049
Polymers54,7934
Non-polymers1,4115
Water7,999444
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-21 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.366, 32.281, 106.963
Angle α, β, γ (deg.)90.00, 125.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-407-

HOH

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Components

#1: Protein
Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13698.247 Da / Num. of mol.: 4 / Mutation: K7H, R10H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Plasmid: pET11c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-C3P / CYTIDINE-3'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 4 / Mutation: K7H, R10H
Source method: isolated from a genetically manipulated source
Formula: C9H14N3O8P / Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: pET11c / Production host: Escherichia coli BL21 (bacteria) / References: EC: 3.1.27.5
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 800 uL crystallisation condition reservoir formed by 27% PEG4000 and 20 mM sodium cacodylate buffer, pH 5.0. Crystals grew from droplets of 1 uL of protein solution and an equal volume of reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.987 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→86.71 Å / Num. all: 84648 / Num. obs: 26449 / % possible obs: 99.4 % / Redundancy: 3.2 % / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RPF

1rpf


Resolution: 2.1→29.125 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3212 1332 5.04 %
Rwork0.2236 --
obs0.2285 26433 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→29.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 8 444 4340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093990
X-RAY DIFFRACTIONf_angle_d1.2125391
X-RAY DIFFRACTIONf_dihedral_angle_d14.4891427
X-RAY DIFFRACTIONf_chiral_restr0.049599
X-RAY DIFFRACTIONf_plane_restr0.006696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0991-2.17410.35331250.2594240897
2.1741-2.26110.36251140.26742515100
2.2611-2.36390.43481350.26932494100
2.3639-2.48850.38631360.2592541100
2.4885-2.64430.36981200.26942495100
2.6443-2.84830.39531310.26562513100
2.8483-3.13470.37821380.2472520100
3.1347-3.58750.28361580.20052517100
3.5875-4.51720.24681340.1762254199
4.51720.27491410.197255796

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