[English] 日本語
Yorodumi
- PDB-3wyz: On archaeal homologs of the human RNase P protein Rpp30 in the hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wyz
TitleOn archaeal homologs of the human RNase P protein Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis
ComponentsRibonuclease P protein component 3
KeywordsHYDROLASE / TIM barrel-like structure / pre-tRNA cleavage / RNA binding
Function / homology
Function and homology information


ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease P, protein component 3, archaeal / RNase P subunit p30 / RNase P subunit p30 / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component 3
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSuematsu, K. / Ueda, T. / Nakashima, T. / Kakuta, Y. / Kimura, M.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2015
Title: On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis.
Authors: Suematsu, K. / Ueda, T. / Nakashima, T. / Kakuta, Y. / Kimura, M.
History
DepositionSep 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 P protein component 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3982
Polymers25,3061
Non-polymers921
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.610, 58.725, 43.280
Angle α, β, γ (deg.)90.00, 109.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribonuclease P protein component 3 / RNase P component 3 / Rpp30


Mass: 25306.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: rnp3, TK1450 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JH47, ribonuclease P
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 283 K / Method: purification / pH: 7.5
Details: 50mM Tris-HCl (pH 7.5), 200mM NaCl, 10mM MgCl2, Purification, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9422 / Num. obs: 9422 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 18.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 2.7 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→33.48 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.894 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.51 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28136 431 4.7 %RANDOM
Rwork0.21901 ---
all0.22191 8799 --
obs0.22191 8799 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.04 Å2
2---0.04 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.21→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 6 39 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191775
X-RAY DIFFRACTIONr_bond_other_d0.0010.021747
X-RAY DIFFRACTIONr_angle_refined_deg0.9391.9722394
X-RAY DIFFRACTIONr_angle_other_deg0.68634012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08322.09981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9731520
X-RAY DIFFRACTIONr_chiral_restr0.050.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_mcbond_it1.9715.355851
X-RAY DIFFRACTIONr_mcbond_other1.9715.354850
X-RAY DIFFRACTIONr_mcangle_it3.2688.0241063
X-RAY DIFFRACTIONr_mcangle_other3.2678.0251064
X-RAY DIFFRACTIONr_scbond_it2.2225.802924
X-RAY DIFFRACTIONr_scbond_other2.2225.802924
X-RAY DIFFRACTIONr_scangle_other3.78.5541330
X-RAY DIFFRACTIONr_long_range_B_refined7.22350.7027366
X-RAY DIFFRACTIONr_long_range_B_other7.22350.6987365
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 25 -
Rwork0.332 580 -
obs--83.45 %

+
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