[English] 日本語
Yorodumi
- PDB-5ft9: Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ft9
TitleArabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2)
ComponentsPROTEINACEOUS RNASE P 2
KeywordsHYDROLASE / PROTEINACEOUS RNASE P / PRORP / PPR / TRNA 5' MATURATION
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: 3.05 Å
AuthorsFernandez-Millan, P. / Pinker, F. / Schelcher, C. / Gobert, A. / Giege, P. / Sauter, C.
Citation
Journal: To be Published
Title: Structures of Arabidopsis Nuclear Rnase P Alone and with tRNA Reveal Plasticities
Authors: Pinker, F. / Schelcher, C. / Fernandez-Millan, P. / Gobert, A. / Birck, C. / Roblin, P. / Giege, P. / Sauter, C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystallization and Crystallographic Analysis of an Arabidopsis Nuclear Proteinaceous Rnase P.
Authors: Pinker, F. / Giege, P. / Sauter, C.
History
DepositionJan 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _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: PROTEINACEOUS RNASE P 2
B: PROTEINACEOUS RNASE P 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9934
Polymers120,8622
Non-polymers1312
Water00
1
A: PROTEINACEOUS RNASE P 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4962
Polymers60,4311
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEINACEOUS RNASE P 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4962
Polymers60,4311
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.500, 72.800, 80.300
Angle α, β, γ (deg.)63.10, 72.20, 78.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.9138, 0.4062, 0.007688), (0.4062, 0.9138, -0.005994), (-0.00946, -0.002355, -1)
Vector: 14.62, 12.05, 64.25)

-
Components

#1: Protein PROTEINACEOUS RNASE P 2 / PROTEIN-ONLY RNASE P


Mass: 60431.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / 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
Nonpolymer detailsZINC ION (ZN): STRUCTURAL ZINC DOMAIN
Sequence detailsADDITION OF A GLY IN SECOND POSITION AND LEHHHHHH C- TERMINAL TAG FOR AFFINITY PURIFICATION

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.4 % / Description: NONE
Crystal growTemperature: 277 K / Method: microbatch / pH: 6
Details: PRORP2 STOCK SOLUTION WAS PREPARED AT 2.5 MG/ML IN 50 MM HEPES-NA PH 7.5, 250 MM NACL, 5%(W/V) GLYCEROL, 1 MM TCEP. PRORP2 WAS CRYSTALLIZED AT 277 K IN 2 MICROLITER MICROBATCH DROPS SET UP ...Details: PRORP2 STOCK SOLUTION WAS PREPARED AT 2.5 MG/ML IN 50 MM HEPES-NA PH 7.5, 250 MM NACL, 5%(W/V) GLYCEROL, 1 MM TCEP. PRORP2 WAS CRYSTALLIZED AT 277 K IN 2 MICROLITER MICROBATCH DROPS SET UP UNDER PARAFIN OIL BY MIXING 1 VOLUME OF PRORP2 SOLUTION WITH 1 VOLUME OF CRYSTALLANT SOLUTION CONTAINING 200 MM SODIUM MALONATE PH 6, 20% (W/V) PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→35 Å / Num. obs: 23923 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 93.61 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.7
Reflection shellResolution: 3.05→3.23 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G26

4g26


Resolution: 3.05→34.707 Å / SU ML: 0.69 / σ(F): 1.91 / Phase error: 43.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 1126 4.8 %
Rwork0.2421 --
obs0.2444 23727 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 145.9 Å2
Refinement stepCycle: LAST / Resolution: 3.05→34.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 2 0 7444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057598
X-RAY DIFFRACTIONf_angle_d1.14810274
X-RAY DIFFRACTIONf_dihedral_angle_d15.0922746
X-RAY DIFFRACTIONf_chiral_restr0.0511125
X-RAY DIFFRACTIONf_plane_restr0.0041315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.18880.44571570.40943005X-RAY DIFFRACTION98
3.1888-3.35670.44331450.39543047X-RAY DIFFRACTION98
3.3567-3.56690.47971310.41582888X-RAY DIFFRACTION95
3.5669-3.84190.47821020.35382168X-RAY DIFFRACTION70
3.8419-4.2280.31411190.2742428X-RAY DIFFRACTION79
4.228-4.83830.26371480.19993025X-RAY DIFFRACTION99
4.8383-6.09040.28111560.21263028X-RAY DIFFRACTION99
6.0904-34.70950.19851680.16683012X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.55372.66320.68274.676-0.12323.15980.0713-0.10490.40660.3065-0.2930.1743-0.4557-0.29540.14251.09990.1057-0.12020.7343-0.11350.430334.219939.822526.0876
23.287-1.1105-0.36943.88061.69288.3254-0.3577-0.42680.34451.27520.0352-0.155-0.4312-0.6640.29211.6104-0.1727-0.1611.0313-0.23090.771618.492517.6401-4.9482
32.3748-1.21360.49147.17380.55392.28690.0582-0.03040.18010.135-0.2218-0.47160.01930.06340.14321.0939-0.3491-0.13040.88430.16190.4747-6.358533.452638.1753
44.63890.19830.52092.20170.17454.8473-0.22930.48690.5213-0.64990.1751-0.0050.08840.7820.05661.6613-0.463-0.06021.21120.25210.7761-0.6386.731769.1332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESID 28 THROUGH 289 ) OR (RESID 479 THROUGH 515))
2X-RAY DIFFRACTION2CHAIN A AND (RESID 290 THROUGH 478 )
3X-RAY DIFFRACTION3CHAIN B AND ((RESID 28 THROUGH 289 ) OR (RESID 479 THROUGH 515))
4X-RAY DIFFRACTION4CHAIN A

+
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