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- PDB-5oab: A novel crystal form of human RNase6 at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 5oab
TitleA novel crystal form of human RNase6 at atomic resolution
ComponentsRibonuclease K6
KeywordsHYDROLASE / RNASE K6 / PANCREATIC RIBONUCLEASE
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
: / PHOSPHATE ION / Ribonuclease K6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.111 Å
AuthorsPrats-Ejarque, G. / Moussaoui, M. / Boix, E.
Funding support Spain, 2items
OrganizationGrant numberCountry
MINECOSAF2015-66007-P Spain
Generalitat de Catalunya2014 SGR 728 Spain
Citation
Journal: 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.
#1: Journal: Biochem. J. / Year: 2016
Title: The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement.
Authors: Prats-Ejarque, G. / Arranz-Trullen, J. / Blanco, J.A. / Pulido, D. / Nogues, M.V. / Moussaoui, M. / Boix, E.
History
DepositionJun 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / 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
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 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 K6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,59114
Polymers14,8071
Non-polymers78413
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-83 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.405, 95.405, 95.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-533-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribonuclease K6 / RNase K6


Mass: 14807.069 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE6, RNS6 / Plasmid: PET11C / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: Q93091, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Non-polymers , 5 types, 322 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.87 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.3 M SODIUM/POTASSIUM PHOSPHATE / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2016
Details: VERTICAL FOCUSING MIRROR (VFM) AND A HORIZONTAL FOCUSING MIRROR (HFM), MANUFACTURED BY IRELEC
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.111→47.703 Å / Num. obs: 54593 / % possible obs: 96.2 % / Redundancy: 4 % / Biso Wilson estimate: 9.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08221 / Rpim(I) all: 0.04389 / Rrim(I) all: 0.0937 / Net I/σ(I): 9.1
Reflection shellResolution: 1.111→1.151 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.6556 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4253 / CC1/2: 0.544 / Rpim(I) all: 0.4686 / Rrim(I) all: 0.8125 / % possible all: 75.17

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS20151001data reduction
Aimless0.5.17data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X09

4x09


Resolution: 1.111→47.703 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1412 2557 4.68 %2554
Rwork0.1173 ---
obs0.1184 54583 96.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.76 Å2
Refinement stepCycle: LAST / Resolution: 1.111→47.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 37 309 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091272
X-RAY DIFFRACTIONf_angle_d1.1021760
X-RAY DIFFRACTIONf_dihedral_angle_d13.696487
X-RAY DIFFRACTIONf_chiral_restr0.099174
X-RAY DIFFRACTIONf_plane_restr0.008232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.111-1.13240.3106940.27982121X-RAY DIFFRACTION71
1.1324-1.15550.27521030.23952483X-RAY DIFFRACTION82
1.1555-1.18060.25591340.20682660X-RAY DIFFRACTION90
1.1806-1.20810.22421480.19832820X-RAY DIFFRACTION95
1.2081-1.23830.19741660.17372935X-RAY DIFFRACTION99
1.2383-1.27180.19781320.15442974X-RAY DIFFRACTION100
1.2718-1.30920.16641490.1422961X-RAY DIFFRACTION100
1.3092-1.35150.15281140.12943018X-RAY DIFFRACTION99
1.3515-1.39980.17291440.1182990X-RAY DIFFRACTION99
1.3998-1.45580.14321490.10542938X-RAY DIFFRACTION99
1.4558-1.52210.12871610.10132972X-RAY DIFFRACTION100
1.5221-1.60230.13491460.08883003X-RAY DIFFRACTION100
1.6023-1.70270.11571680.08942985X-RAY DIFFRACTION100
1.7027-1.83420.12761230.09283032X-RAY DIFFRACTION100
1.8342-2.01880.12811640.0932985X-RAY DIFFRACTION100
2.0188-2.31090.10271760.09032991X-RAY DIFFRACTION100
2.3109-2.91150.12041490.10713047X-RAY DIFFRACTION100
2.9115-47.74650.13591370.11873111X-RAY DIFFRACTION99

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