[English] 日本語
Yorodumi
- PDB-5ws2: Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ws2
TitleCrystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*A)-3')
  • Ribonuclease J
KeywordsHYDROLASE / EXORIBONUCLEASE / BETA-CASP / MBL
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA catabolic process / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease J, archaea / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
RNA / Ribonuclease J
Similarity search - Component
Biological speciesMethanolobus psychrophilus R15 (archaea)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsLi, D.F. / Feng, N.
CitationJournal: Mol. Microbiol. / Year: 2017
Title: New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family
Authors: Zheng, X. / Feng, N. / Li, D. / Dong, X. / Li, J.
History
DepositionDec 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease J
B: Ribonuclease J
C: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,65717
Polymers107,5314
Non-polymers1,12613
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-297 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.610, 168.610, 165.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Ribonuclease J / RNase J


Mass: 52164.453 Da / Num. of mol.: 2 / Mutation: S247A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanolobus psychrophilus R15 (archaea)
Gene: rnj, Mpsy_0886 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: K4MAF9, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*A)-3')


Mass: 1601.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01M MgSO4, 0.05M Sodium cacodylate trihydrate, 2M (NH4)2SO4
PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 54889 / % possible obs: 100 % / Redundancy: 16.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 5 / CC1/2: 0.903 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAB
Resolution: 2.398→48.674 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2000 3.68 %Random
Rwork0.1731 ---
obs0.1745 54405 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→48.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7207 222 49 312 7790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097628
X-RAY DIFFRACTIONf_angle_d1.18210384
X-RAY DIFFRACTIONf_dihedral_angle_d23.4212848
X-RAY DIFFRACTIONf_chiral_restr0.0751185
X-RAY DIFFRACTIONf_plane_restr0.0091306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3976-2.45760.26631390.21393667X-RAY DIFFRACTION99
2.4576-2.5240.29391420.20693702X-RAY DIFFRACTION100
2.524-2.59830.28031420.1943716X-RAY DIFFRACTION100
2.5983-2.68220.25561410.20013692X-RAY DIFFRACTION100
2.6822-2.7780.21151420.20063723X-RAY DIFFRACTION100
2.778-2.88920.26581420.20413714X-RAY DIFFRACTION100
2.8892-3.02070.23031420.19223738X-RAY DIFFRACTION100
3.0207-3.180.23361440.18833748X-RAY DIFFRACTION100
3.18-3.37910.20021430.17623760X-RAY DIFFRACTION100
3.3791-3.640.22641440.17093758X-RAY DIFFRACTION100
3.64-4.00610.21261440.16133787X-RAY DIFFRACTION100
4.0061-4.58540.16331450.13953783X-RAY DIFFRACTION100
4.5854-5.77570.17571440.15393801X-RAY DIFFRACTION98
5.7757-48.68350.17351460.17053816X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1298-0.73142.10521.3564-0.62823.28680.20550.3372-0.1734-0.0936-0.25590.04070.21970.3230.04680.29610.08270.0920.35630.0150.315964.805344.92491.685
21.1089-0.266-0.08410.8550.01151.2395-0.01020.1798-0.1594-0.1449-0.03650.01360.27530.01340.04090.30230.0340.0320.2579-0.06160.264243.1332345.083-3.2132
34.5533-1.36633.35130.3946-1.02612.4263-0.3247-0.2478-0.28880.03810.54960.0817-0.3829-0.3409-0.19750.3515-0.0270.00270.5541-0.00780.397-7.0913380.09596.0492
42.5221.2546-1.29163.63190.40331.66120.1059-0.2641-0.03790.3109-0.1022-0.0363-0.0478-0.14870.00090.2520.05550.05840.55550.03640.275813.3254365.51534.4229
51.8705-0.6952-0.52162.54680.10480.28160.0077-0.00710.02920.24470.01450.2170.0727-0.4606-0.01330.2433-0.03960.07890.56790.01160.39235.913356.561824.9107
61.8617-1.37320.9052.5985-1.30221.9746-0.03820.0061-0.3069-0.02650.07610.17370.3206-0.3904-0.03670.2472-0.07640.0850.3417-0.02660.318621.8115345.206121.2942
74.10520.62130.16861.97440.35382.42110.0312-0.5784-0.35310.4648-0.02420.12310.4633-0.1381-0.030.40270.02410.07910.31410.08670.300533.5006340.941335.0276
80.26230.0109-0.28850.01560.02130.3636-0.06460.03790.1940.05010.0114-0.0320.04610.00420.04110.24270.04410.02370.2928-0.0020.316337.665352.454425.6156
92.11440.3859-0.37242.71490.34520.8372-0.07780.17930.1477-0.10980.00650.2877-0.1484-0.48340.09070.20190.0836-0.00030.51080.06470.278412.5125370.012611.8931
106.2-1.52945.05245.0324-2.08235.3973-0.22250.48670.56040.397-0.2774-0.45290.19981.08110.45120.59930.1245-0.06780.595-0.0730.741642.1543353.0719-8.7553
117.0826-3.88066.99936.016-2.72847.2724-0.24510.20330.48520.80990.36960.2731-1.4338-0.6361-0.160.52780.01410.10770.49970.03360.715826.1595355.710332.7203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -19 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 448 )
3X-RAY DIFFRACTION3chain 'B' and (resid -14 through 10 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 118 )
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 282 )
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 358 )
8X-RAY DIFFRACTION8chain 'B' and (resid 359 through 390 )
9X-RAY DIFFRACTION9chain 'B' and (resid 391 through 448 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 5 )

+
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