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- PDB-6mv7: Crystal structure of RNAse 6 -

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Basic information

Entry
Database: PDB / ID: 6mv7
TitleCrystal structure of RNAse 6
ComponentsRibonuclease K6
KeywordsHYDROLASE / rnase / nuclease
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / defense response / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cytoplasmic vesicle / endonuclease activity / defense response to Gram-negative bacterium ...Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / defense response / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cytoplasmic vesicle / endonuclease activity / defense response to Gram-negative bacterium / defense response to virus / nucleic acid binding / lysosome / defense response to Gram-positive bacterium / innate immune response / extracellular space / 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
ADENOSINE MONOPHOSPHATE / Ribonuclease K6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsCouture, J.-F. / Doucet, N.
CitationJournal: Biochemistry / Year: 2020
Title: Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding.
Authors: Narayanan, C. / Bernard, D.N. / Letourneau, M. / Gagnon, J. / Gagne, D. / Bafna, K. / Calmettes, C. / Couture, J.F. / Agarwal, P.K. / Doucet, N.
History
DepositionOct 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 2.0Jan 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Refinement description / Structure summary
Category: atom_site / computing ...atom_site / computing / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software
Item: _pdbx_nonpoly_scheme.auth_seq_num / _refine.B_iso_max ..._pdbx_nonpoly_scheme.auth_seq_num / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _reflns.B_iso_Wilson_estimate / _reflns_shell.number_unique_obs / _software.version
Description: Polymer geometry / Details: Few ramachandran outliers were fixed. / Provider: author / Type: Coordinate replacement
Revision 2.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 2.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Ribonuclease K6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1542
Polymers14,8071
Non-polymers3471
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.650, 38.830, 97.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease K6 / RNase K6


Mass: 14807.069 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE6, RNS6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93091, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 30.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 4000, 50mM Sodium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→36.1 Å / Num. obs: 3537 / % possible obs: 98.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 14.86 Å2 / Rsym value: 0.046 / Net I/σ(I): 17.2
Reflection shellResolution: 2.6→2.71 Å / Num. unique obs: 308 / Rsym value: 0.104

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MV6

6mv6


Resolution: 2.59→36.095 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.28
RfactorNum. reflection% reflection
Rfree0.2519 354 10.01 %
Rwork0.2168 --
obs0.2204 3537 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.57 Å2 / Biso mean: 19.0356 Å2 / Biso min: 3.81 Å2
Refinement stepCycle: final / Resolution: 2.59→36.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 23 27 1063
Biso mean--32.27 17.32 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031083
X-RAY DIFFRACTIONf_angle_d0.7031481
X-RAY DIFFRACTIONf_chiral_restr0.041157
X-RAY DIFFRACTIONf_plane_restr0.004189
X-RAY DIFFRACTIONf_dihedral_angle_d13.497660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.59-2.96450.29311130.246101397
2.9645-3.73430.26731150.219103899
3.7343-36.0950.21981260.19981132100

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