[English] 日本語
Yorodumi
- PDB-8yyj: RNase J2 mutant H80A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yyj
TitleRNase J2 mutant H80A
ComponentsRibonuclease J 2
KeywordsRNA BINDING PROTEIN / Ribonuclease / RNase J2
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
: / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP 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 ...: / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP 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
Similarity search - Domain/homology
: / Ribonuclease J 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSingh, A.K. / Chinnasamy, K. / Gopal, B.
Funding support India, 3items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)FA/DSTO-17-0001.03 India
Department of Science & Technology (DST, India)SP/DSTO-16-1668.03 India
Science and Engineering Research Board (SERB)SP/SERB-23-0307.26 India
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A physicochemical rationale for the varied catalytic efficiency in RNase J paralogues.
Authors: Singh, A.K. / Chinnasamy, K. / Pahelkar, N.R. / Gopal, B.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease J 2
B: Ribonuclease J 2
C: Ribonuclease J 2
D: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,4698
Polymers257,2494
Non-polymers2204
Water1448
1
A: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3672
Polymers64,3121
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3672
Polymers64,3121
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3672
Polymers64,3121
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3672
Polymers64,3121
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.890, 131.910, 116.190
Angle α, β, γ (deg.)90.000, 91.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ribonuclease J 2 / RNase J2


Mass: 64312.258 Da / Num. of mol.: 4 / Mutation: H80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: rnj2, SERP0842 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5HPR6, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.6
Details: 100mM tri-sodium citrate dihydrate pH 5.6, 20% PEG 4000, 20% Isopropanol, 40% Formamide
PH range: 5.6-6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 3→66 Å / Num. obs: 35724 / % possible obs: 91.3 % / Redundancy: 3 % / CC1/2: 0.96 / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / Num. unique obs: 5223 / CC1/2: 0.67 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→66 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.783 / SU B: 27.342 / SU ML: 0.484 / Cross valid method: FREE R-VALUE / ESU R Free: 0.589
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2998 1738 4.894 %
Rwork0.2473 33772 -
all0.25 --
obs-35510 90.589 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.353 Å2
Baniso -1Baniso -2Baniso -3
1-0.634 Å2-0 Å2-0.411 Å2
2--0.05 Å2-0 Å2
3----0.658 Å2
Refinement stepCycle: LAST / Resolution: 3→66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13096 0 4 8 13108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01213356
X-RAY DIFFRACTIONr_bond_other_d0.0040.01612189
X-RAY DIFFRACTIONr_angle_refined_deg1.121.62518104
X-RAY DIFFRACTIONr_angle_other_deg0.391.54828195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71451751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.1711038
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.329102148
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.33410533
X-RAY DIFFRACTIONr_chiral_restr0.0450.22102
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215221
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022532
X-RAY DIFFRACTIONr_nbd_refined0.2140.22645
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.211890
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26579
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.26852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2208
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.227
X-RAY DIFFRACTIONr_nbd_other0.2670.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.23
X-RAY DIFFRACTIONr_mcbond_it2.7344.2547022
X-RAY DIFFRACTIONr_mcbond_other2.7344.2547022
X-RAY DIFFRACTIONr_mcangle_it4.5816.3738767
X-RAY DIFFRACTIONr_mcangle_other4.5816.3738768
X-RAY DIFFRACTIONr_scbond_it2.3734.1976334
X-RAY DIFFRACTIONr_scbond_other2.3734.1976335
X-RAY DIFFRACTIONr_scangle_it3.9856.2649337
X-RAY DIFFRACTIONr_scangle_other3.9856.2649338
X-RAY DIFFRACTIONr_lrange_it9.19978.37654601
X-RAY DIFFRACTIONr_lrange_other9.19978.3854599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0780.3531170.3032523X-RAY DIFFRACTION91.6667
3.078-3.1620.4121110.2992465X-RAY DIFFRACTION93.03
3.162-3.2530.3361320.2812447X-RAY DIFFRACTION93.3068
3.253-3.3530.3621240.2672357X-RAY DIFFRACTION94.2987
3.353-3.4630.2681040.2611810X-RAY DIFFRACTION73.7857
3.463-3.5840.3631030.2782120X-RAY DIFFRACTION89.0625
3.584-3.7190.571770.5031467X-RAY DIFFRACTION64.5485
3.719-3.870.3191040.2922112X-RAY DIFFRACTION95.0665
3.87-4.0420.258980.2581519X-RAY DIFFRACTION73.2005
4.042-4.2380.2411160.2061944X-RAY DIFFRACTION96.759
4.238-4.4670.2541000.2051856X-RAY DIFFRACTION97.1684
4.467-4.7360.203860.1771791X-RAY DIFFRACTION97.3043
4.736-5.0610.222620.1771702X-RAY DIFFRACTION97.1901
5.061-5.4640.275960.1961545X-RAY DIFFRACTION97.6205
5.464-5.9820.242710.2171430X-RAY DIFFRACTION97.5943
5.982-6.6810.364510.251326X-RAY DIFFRACTION98.0769
6.681-7.7010.271590.2131154X-RAY DIFFRACTION97.8226
7.701-9.40.208530.1571000X-RAY DIFFRACTION98.2276
9.4-13.1610.251380.172777X-RAY DIFFRACTION98.1928
13.161-660.483360.432427X-RAY DIFFRACTION96.4583

+
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