[English] 日本語
Yorodumi
- PDB-5diz: Crystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5diz
TitleCrystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) from A. thaliana
ComponentsProteinaceous RNase P 2
KeywordsHYDROLASE / RNA BINDING PROTEIN / Metallonuclease / PRORP / Ribonuclease / tRNA processing / Rnase P / NYN domain / PPR domain / nucleus
Function / homology
Function and homology information


sno(s)RNA processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / mRNA processing / nucleus / metal ion binding
Similarity search - Function
Rossmann fold - #11980 / Protein-only RNase P, C-terminal / Protein-only RNase P / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold ...Rossmann fold - #11980 / Protein-only RNase P, C-terminal / Protein-only RNase P / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proteinaceous RNase P 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKarasik, A. / Shanmuganathan, A. / Howard, M.J. / Fierke, C.A. / Koutmos, M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes.
Authors: Karasik, A. / Shanmuganathan, A. / Howard, M.J. / Fierke, C.A. / Koutmos, M.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteinaceous RNase P 2
B: Proteinaceous RNase P 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2814
Polymers119,1502
Non-polymers1312
Water905
1
A: Proteinaceous RNase P 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6412
Polymers59,5751
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proteinaceous RNase P 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6412
Polymers59,5751
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.980, 76.993, 80.112
Angle α, β, γ (deg.)72.66, 64.11, 77.76
Int Tables number1
Space group name H-MP1
DetailsMonomer by Analytical ultracentrifugation

-
Components

#1: Protein Proteinaceous RNase P 2


Mass: 59575.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRORP2, At2g16650, T24I21.6 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q680B9, ribonuclease P
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.8 / Details: 19.9 % (w/v) PEG3000, and 0.21 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2014
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 23244 / % possible obs: 99.1 % / Redundancy: 2 % / Rsym value: 0.059 / Net I/σ(I): 8.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.4 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G24

4g24


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 36.722 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27171 1150 4.9 %RANDOM
Rwork0.22821 ---
obs0.23042 22090 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 123.153 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20.33 Å23.92 Å2
2--15.57 Å2-4.02 Å2
3----8.17 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7479 0 2 5 7486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197653
X-RAY DIFFRACTIONr_bond_other_d0.0010.027302
X-RAY DIFFRACTIONr_angle_refined_deg0.971.94410350
X-RAY DIFFRACTIONr_angle_other_deg0.8433.00216599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2965944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59124.451364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.874151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6321542
X-RAY DIFFRACTIONr_chiral_restr0.0540.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021770
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.38912.2683782
X-RAY DIFFRACTIONr_mcbond_other2.38812.2673781
X-RAY DIFFRACTIONr_mcangle_it4.17618.3954718
X-RAY DIFFRACTIONr_mcangle_other4.17618.3954719
X-RAY DIFFRACTIONr_scbond_it1.79712.393871
X-RAY DIFFRACTIONr_scbond_other1.79712.3913872
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.28918.5185631
X-RAY DIFFRACTIONr_long_range_B_refined6.18596.6628624
X-RAY DIFFRACTIONr_long_range_B_other6.18596.678625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 78 -
Rwork0.364 1506 -
obs--93.34 %

+
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