[English] 日本語
Yorodumi
- PDB-5mpy: Crystal structure of Arabidopsis thaliana RNA editing factor MORF9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mpy
TitleCrystal structure of Arabidopsis thaliana RNA editing factor MORF9
ComponentsMultiple organellar RNA editing factor 9, chloroplastic
KeywordsPLANT PROTEIN / NFLD-related fold
Function / homology
Function and homology information


chloroplast RNA modification / cytidine to uridine editing / chloroplast envelope / chloroplast stroma / chloroplast / mRNA processing / protein dimerization activity / mRNA binding / protein homodimerization activity
Similarity search - Function
MORF/ORRM1/DAG-like / : / Multiple organellar RNA editing factor 1, MORF domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily
Similarity search - Domain/homology
Multiple organellar RNA editing factor 9, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 Å
AuthorsHaag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9.
Authors: Haag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G.
History
DepositionDec 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multiple organellar RNA editing factor 9, chloroplastic
B: Multiple organellar RNA editing factor 9, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2326
Polymers23,0722
Non-polymers1604
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-49 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.875, 73.875, 264.938
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-396-

HOH

-
Components

#1: Protein Multiple organellar RNA editing factor 9, chloroplastic / RNA editing-interacting protein 9


Mass: 11535.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MORF9, RIP9, At1g11430, T23J18.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LPZ1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 4.52 Å3/Da / Density % sol: 72.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.08 M sodium cacodylate, pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol, 0.16 M calcium acetate and 0.04 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.247→50 Å / Num. obs: 21313 / % possible obs: 99.6 % / Redundancy: 10.5 % / Rsym value: 0.09 / Net I/σ(I): 16.99
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.56 / Num. unique all: 3327 / CC1/2: 0.772 / Rsym value: 1.42 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MPW

5mpw


Resolution: 2.247→46.016 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2381 1066 5 %
Rwork0.1951 --
obs0.1973 21308 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.82 Å2 / Biso mean: 59.7022 Å2 / Biso min: 29.13 Å2
Refinement stepCycle: final / Resolution: 2.247→46.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 4 157 1783
Biso mean--63.78 58.37 -
Num. residues----202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091686
X-RAY DIFFRACTIONf_angle_d0.9792296
X-RAY DIFFRACTIONf_chiral_restr0.061249
X-RAY DIFFRACTIONf_plane_restr0.006294
X-RAY DIFFRACTIONf_dihedral_angle_d13.8371008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2475-2.34980.34141270.29492420254799
2.3498-2.47370.34191310.287724802611100
2.4737-2.62860.3661300.27424702600100
2.6286-2.83160.35031310.26782489262099
2.8316-3.11640.2951310.234224992630100
3.1164-3.56730.26811340.195325352669100
3.5673-4.49380.18951350.155225702705100
4.4938-46.02580.181470.16372779292699

+
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