[English] 日本語
Yorodumi
- PDB-4g26: Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. tha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g26
TitleCrystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana with Ca
ComponentsPentatricopeptide repeat-containing protein At2g32230, mitochondrial
KeywordsRNA BINDING PROTEIN / Metallonuclease / PRORP / Ribonuclease / PIN / tRNA processing / Rnase P / NYN domain / PPR domain / Chloroplasts
Function / homology
Function and homology information


ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / chloroplast / mitochondrion / 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 / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...Rossmann fold - #11980 / Protein-only RNase P, C-terminal / Protein-only RNase P / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / 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 1, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKoutmos, M. / Howard, M.J. / Fierke, C.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.
Authors: Howard, M.J. / Lim, W.H. / Fierke, C.A. / Koutmos, M.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _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: Pentatricopeptide repeat-containing protein At2g32230, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9277
Polymers56,6611
Non-polymers2666
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.790, 111.883, 140.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pentatricopeptide repeat-containing protein At2g32230, mitochondrial


Mass: 56660.734 Da / Num. of mol.: 1 / Fragment: UNP residues 77-572
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g32230, F22D22.2 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q66GI4, ribonuclease P
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG 3,350, 0.1 M sodium citrate pH 5.5, and 0.02 M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2012
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: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 66940 / Num. obs: 65735 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.075 / Net I/σ(I): 12.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 6596 / Rsym value: 0.544 / % possible all: 88.1

-
Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G23

4g23


Resolution: 1.75→43.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.991 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20872 3319 5.1 %RANDOM
Rwork0.16246 ---
obs0.16483 62354 98.05 %-
all-65673 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--1.79 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 6 384 4177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193916
X-RAY DIFFRACTIONr_bond_other_d0.0020.023789
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9535300
X-RAY DIFFRACTIONr_angle_other_deg0.8383.0028642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1124.202188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65815707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.231529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
X-RAY DIFFRACTIONr_rigid_bond_restr5.57832284
X-RAY DIFFRACTIONr_sphericity_free22.12251
X-RAY DIFFRACTIONr_sphericity_bonded22.64552229
LS refinement shellResolution: 1.75→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 185 -
Rwork0.249 3658 -
obs--82.86 %

+
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