[English] 日本語
Yorodumi
- PDB-5a0t: Catalysis and 5' end sensing by ribonuclease RNase J of the metal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a0t
TitleCatalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family
Components
  • 5'-R(*CP*GP*CP*CP*UP)-3'
  • RIBONUCLEASE J
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / RIBONUCLEASE / RNASE J / ENDONUCLEASE / EXONUCLEASE
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily ...Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA / Ribonuclease J
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR A3
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.283 Å
AuthorsPei, X.Y. / Bralley, P. / Jones, G.H. / Luisi, B.F.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J
Authors: Pei, X.Y. / Bralley, P. / Jones, G.H. / Luisi, B.F.
History
DepositionApr 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.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_asym_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBONUCLEASE J
B: RIBONUCLEASE J
E: 5'-R(*CP*GP*CP*CP*UP)-3'
F: 5'-R(*CP*GP*CP*CP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,42010
Polymers125,9464
Non-polymers4746
Water10,052558
1
A: RIBONUCLEASE J
E: 5'-R(*CP*GP*CP*CP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2105
Polymers62,9732
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-104.4 kcal/mol
Surface area18650 Å2
MethodPISA
2
B: RIBONUCLEASE J
F: 5'-R(*CP*GP*CP*CP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2105
Polymers62,9732
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-105.1 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.187, 186.187, 113.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-2024-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.01394, 0.002726), (-0.001394, 0.2872, 0.9579), (-0.01414, 0.9578, -0.2872)
Vector: 121.8, -27.14, 37.41)

-
Components

#1: Protein RIBONUCLEASE J


Mass: 61146.090 Da / Num. of mol.: 2
Fragment: BETA-LACTMASE DOMAIN AND BETA-CASP DOMAIN, RESIDUES 1-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR A3(2) (bacteria)
Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: O86842
#2: RNA chain 5'-R(*CP*GP*CP*CP*UP)-3'


Mass: 1827.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: ROSETTA2 PLYSS / Strain: BL21(DE3)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 4.9 Å3/Da / Density % sol: 0.74 % / Description: NONE
Crystal growpH: 8.5
Details: THE BEST CRYSTALS OF S. COELICOLOR RNASE J WERE OBTAINED IN THE 27.5% W/V PEG 400, 0.1 M TRIS-HCL, PH 8.5 BY MIXING A 1:2 VOLUME RATIO OF CRYSTALLIZATION RESERVOIR TO PROTEIN SOLUTION.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2824
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.28→35 Å / Num. obs: 88741 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.6
Reflection shellResolution: 2.28→2.3 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
SHELXphasing
PHENIXphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 3BK1

3bk1


Resolution: 2.283→29.34 Å / SU ML: 0.23 / σ(F): 1.21 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 8404 5 %
Rwork0.1446 --
obs0.1463 88509 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.283→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6950 216 18 558 7742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097344
X-RAY DIFFRACTIONf_angle_d1.20610019
X-RAY DIFFRACTIONf_dihedral_angle_d13.8122759
X-RAY DIFFRACTIONf_chiral_restr0.0511150
X-RAY DIFFRACTIONf_plane_restr0.0051289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2826-2.30850.31231900.27063448X-RAY DIFFRACTION63
2.3085-2.33570.32372320.26074622X-RAY DIFFRACTION85
2.3357-2.36420.26322620.24884852X-RAY DIFFRACTION88
2.3642-2.39410.29892430.23875052X-RAY DIFFRACTION92
2.3941-2.42560.2482620.23295222X-RAY DIFFRACTION95
2.4256-2.45880.21272720.21245397X-RAY DIFFRACTION99
2.4588-2.49390.22942810.20245417X-RAY DIFFRACTION99
2.4939-2.53110.21742640.1815476X-RAY DIFFRACTION100
2.5311-2.57060.23422730.17165493X-RAY DIFFRACTION100
2.5706-2.61270.23672810.16575466X-RAY DIFFRACTION100
2.6127-2.65780.19033180.16495461X-RAY DIFFRACTION100
2.6578-2.70610.21733160.17075454X-RAY DIFFRACTION100
2.7061-2.75810.22932610.17585532X-RAY DIFFRACTION100
2.7581-2.81430.21292650.17595447X-RAY DIFFRACTION100
2.8143-2.87550.18492900.15715461X-RAY DIFFRACTION100
2.8755-2.94230.20332990.15635422X-RAY DIFFRACTION99
2.9423-3.01580.20682760.15455504X-RAY DIFFRACTION100
3.0158-3.09730.19362960.16255454X-RAY DIFFRACTION100
3.0973-3.18830.21222870.17055498X-RAY DIFFRACTION100
3.1883-3.29110.1842510.15945500X-RAY DIFFRACTION100
3.2911-3.40850.17342480.15925531X-RAY DIFFRACTION100
3.4085-3.54480.20623270.14925356X-RAY DIFFRACTION99
3.5448-3.70580.18353120.1445429X-RAY DIFFRACTION99
3.7058-3.90080.15583010.12835428X-RAY DIFFRACTION100
3.9008-4.14450.13512770.11265458X-RAY DIFFRACTION99
4.1445-4.46350.12573560.10335354X-RAY DIFFRACTION99
4.4635-4.91080.12542590.09985436X-RAY DIFFRACTION99
4.9108-5.61710.1582970.1085434X-RAY DIFFRACTION99
5.6171-7.06060.16953400.12945397X-RAY DIFFRACTION99
7.0606-29.34260.17972680.15865421X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5496-0.2050.15420.9115-0.33261.8589-0.0230.1333-0.0826-0.1144-0.00160.02010.1469-0.15870.03470.2605-0.00760.03610.53440.00190.384567.6969-5.51110.6344
20.49840.13380.13981.587-0.42311.2773-0.02860.1307-0.1489-0.16340.03330.0410.2931-0.3659-0.0060.332-0.1420.05320.54950.00230.421954.6363-28.154931.201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

+
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://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