[English] 日本語
Yorodumi
- PDB-5hab: Crystal structure of mpy-RNase J (mutant H84A), an archaeal RNase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hab
TitleCrystal structure of mpy-RNase J (mutant H84A), 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 / RNase J
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, D.F. / Feng, N.
CitationJournal: To Be Published
Title: Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1
Authors: Zheng, X. / Feng, N. / Li, D.F. / Li, J. / Dong, X.Z.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 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)108,29313
Polymers107,4294
Non-polymers8659
Water5,080282
1
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

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)216,58726
Polymers214,8588
Non-polymers1,72918
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area22600 Å2
ΔGint-322 kcal/mol
Surface area67530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.680, 169.680, 167.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-725-

HOH

-
Components

#1: Protein Ribonuclease J / RNase J


Mass: 52113.383 Da / Num. of mol.: 2 / Fragment: UNP residues 2-448 / Mutation: H84A
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.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8M ammonium sulfate, 3% glycerol / PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: PHILLIPS / Detector: PIXEL / Date: May 18, 2015
RadiationMonochromator: doubel crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.3→84.84 Å / Num. obs: 63078 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXDEV_1980refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→55.21 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 3119 4.95 %
Rwork0.206 --
obs0.208 63052 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7142 222 45 282 7691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057560
X-RAY DIFFRACTIONf_angle_d0.93710291
X-RAY DIFFRACTIONf_dihedral_angle_d14.1272822
X-RAY DIFFRACTIONf_chiral_restr0.0431178
X-RAY DIFFRACTIONf_plane_restr0.0041293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33590.36061340.29692696X-RAY DIFFRACTION100
2.3359-2.37420.32761370.27552678X-RAY DIFFRACTION100
2.3742-2.41520.31531290.27552706X-RAY DIFFRACTION100
2.4152-2.45910.33461340.26822706X-RAY DIFFRACTION100
2.4591-2.50640.32671120.26422730X-RAY DIFFRACTION100
2.5064-2.55760.30991340.24512694X-RAY DIFFRACTION100
2.5576-2.61320.27371270.24192709X-RAY DIFFRACTION100
2.6132-2.67390.31581410.25522684X-RAY DIFFRACTION100
2.6739-2.74080.30371540.25492704X-RAY DIFFRACTION100
2.7408-2.81490.31151250.25692699X-RAY DIFFRACTION100
2.8149-2.89770.2961520.24112706X-RAY DIFFRACTION100
2.8977-2.99130.30021570.23782699X-RAY DIFFRACTION100
2.9913-3.09820.29141420.22342710X-RAY DIFFRACTION100
3.0982-3.22220.27651440.22232714X-RAY DIFFRACTION100
3.2222-3.36880.22571560.21312686X-RAY DIFFRACTION100
3.3688-3.54640.25981440.20662740X-RAY DIFFRACTION100
3.5464-3.76860.20841550.19362713X-RAY DIFFRACTION99
3.7686-4.05950.22191540.18212728X-RAY DIFFRACTION99
4.0595-4.46780.21141440.16592755X-RAY DIFFRACTION99
4.4678-5.11390.1681350.15552767X-RAY DIFFRACTION99
5.1139-6.44140.21791420.18882797X-RAY DIFFRACTION99
6.4414-55.22170.19461670.18732912X-RAY DIFFRACTION97

+
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