[English] 日本語
Yorodumi
- PDB-5i9f: Crystal structure of designed pentatricopeptide repeat protein dP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i9f
TitleCrystal structure of designed pentatricopeptide repeat protein dPPR-U10 in complex with its target RNA U10
Components
  • RNA (5'-R(*GP*GP*GP*GP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*CP*CP*C)-3')
  • pentatricopeptide repeat protein dPPR-U10
KeywordsRNA BINDING PROTEIN/RNA / single-stranded RNA / designer pentatricopeptide repeat protein / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsShen, C. / Zhang, D. / Guan, Z. / Zou, T. / Yin, Y.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.
Authors: Shen, C. / Zhang, D. / Guan, Z. / Liu, Y. / Yang, Z. / Yang, Y. / Wang, X. / Wang, Q. / Zhang, Q. / Fan, S. / Zou, T. / Yin, P.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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: pentatricopeptide repeat protein dPPR-U10
F: RNA (5'-R(*GP*GP*GP*GP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)57,1372
Polymers57,1372
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-37 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.732, 85.266, 95.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein pentatricopeptide repeat protein dPPR-U10 /


Mass: 51518.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: RNA chain RNA (5'-R(*GP*GP*GP*GP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Mass: 5618.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.87 Å3/Da / Density % sol: 34.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Bis-Tris propane, Magnesium chloride, Ethyl Acetate,D-(+)-glucose monohydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection% possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 21.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PJR

4pjr


Resolution: 2.194→38.903 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.36
RfactorNum. reflection% reflection
Rfree0.2994 1088 4.89 %
Rwork0.2503 --
obs0.2527 22260 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.194→38.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 204 0 76 3270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013248
X-RAY DIFFRACTIONf_angle_d1.2414414
X-RAY DIFFRACTIONf_dihedral_angle_d17.3611279
X-RAY DIFFRACTIONf_chiral_restr0.058536
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.29410.33331130.29632536X-RAY DIFFRACTION96
2.2941-2.4150.34191140.2882663X-RAY DIFFRACTION100
2.415-2.56630.34711570.29762616X-RAY DIFFRACTION100
2.5663-2.76440.37931400.28632639X-RAY DIFFRACTION100
2.7644-3.04250.31191240.26292655X-RAY DIFFRACTION100
3.0425-3.48250.31061470.25642676X-RAY DIFFRACTION100
3.4825-4.38670.28271550.2082667X-RAY DIFFRACTION99
4.3867-38.90910.26771380.24922720X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -10.1919 Å / Origin y: -1.2612 Å / Origin z: 27.6809 Å
111213212223313233
T0.3078 Å20.017 Å2-0.0284 Å2-0.3427 Å2-0.0014 Å2--0.3875 Å2
L0.0425 °20.4113 °2-0.1953 °2-0.84 °2-0.4723 °2--2.4826 °2
S-0.0638 Å °0.027 Å °0.0064 Å °-0.0608 Å °0.0381 Å °-0.0766 Å °0.1633 Å °0.2354 Å °0.0218 Å °
Refinement TLS groupSelection details: ALL

+
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