[English] 日本語
Yorodumi
- PDB-5oab: A novel crystal form of human RNase6 at atomic resolution -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more