[English] 日本語
Yorodumi
- PDB-7e8o: Crystal structure of proteinaceous RNase P(PRORP) from Planctomyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e8o
TitleCrystal structure of proteinaceous RNase P(PRORP) from Planctomycetes bacterium GWF2_40_8 complexed with Escherichia coli histidine pre-tRNA
Components
  • RNA-free ribonuclease P
  • histidine pre-tRNA
KeywordsHYDROLASE / complex / proteinaceous RNase P / PRORP / metallonuclease / tRNA 5' maturation / pre-tRNA processing
Function / homology
Function and homology information


ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / ligase activity / metal ion binding
Similarity search - Function
RNA-free ribonuclease P / PINc domain ribonuclease / PIN-like domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-free ribonuclease P
Similarity search - Component
Biological speciesPlanctomycetes bacterium GWF2_40_8 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsLi, Y.Y. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870721 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structures and insights into precursor tRNA 5'-end processing by prokaryotic minimal protein-only RNase P.
Authors: Li, Y. / Su, S. / Gao, Y. / Lu, G. / Liu, H. / Chen, X. / Shao, Z. / Zhang, Y. / Shao, Q. / Zhao, X. / Yang, J. / Cao, C. / Lin, J. / Ma, J. / Gan, J.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
C: RNA-free ribonuclease P
D: RNA-free ribonuclease P
X: histidine pre-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,48210
Polymers123,2825
Non-polymers2005
Water1629
1
A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
X: histidine pre-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4226
Polymers75,3013
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-77 kcal/mol
Surface area30250 Å2
MethodPISA
2
C: RNA-free ribonuclease P
D: RNA-free ribonuclease P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0614
Polymers47,9802
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-56 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.277, 146.277, 143.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 14 and (name N or name...
21(chain B and ((resid 14 and (name N or name...
31(chain C and ((resid 14 and (name N or name...
41(chain D and (resid 14 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU(chain A and ((resid 14 and (name N or name...AA1419
12ARGARGMETMET(chain A and ((resid 14 and (name N or name...AA10 - 20315 - 208
13ARGARGMETMET(chain A and ((resid 14 and (name N or name...AA10 - 20315 - 208
14ARGARGMETMET(chain A and ((resid 14 and (name N or name...AA10 - 20315 - 208
15ARGARGMETMET(chain A and ((resid 14 and (name N or name...AA10 - 20315 - 208
21GLUGLUGLUGLU(chain B and ((resid 14 and (name N or name...BB1419
22LYSLYSMETMET(chain B and ((resid 14 and (name N or name...BB13 - 20318 - 208
23LYSLYSMETMET(chain B and ((resid 14 and (name N or name...BB13 - 20318 - 208
24LYSLYSMETMET(chain B and ((resid 14 and (name N or name...BB13 - 20318 - 208
25LYSLYSMETMET(chain B and ((resid 14 and (name N or name...BB13 - 20318 - 208
31GLUGLUGLUGLU(chain C and ((resid 14 and (name N or name...CC1419
32ARGARGMETMET(chain C and ((resid 14 and (name N or name...CC10 - 20315 - 208
33ARGARGMETMET(chain C and ((resid 14 and (name N or name...CC10 - 20315 - 208
34ARGARGMETMET(chain C and ((resid 14 and (name N or name...CC10 - 20315 - 208
35ARGARGMETMET(chain C and ((resid 14 and (name N or name...CC10 - 20315 - 208
41GLUGLUGLYGLY(chain D and (resid 14 through 34 or (resid 35...DD14 - 3419 - 39
42ARGARGARGARG(chain D and (resid 14 through 34 or (resid 35...DD3540
43GLUGLUMETMET(chain D and (resid 14 through 34 or (resid 35...DD14 - 20319 - 208
44GLUGLUMETMET(chain D and (resid 14 through 34 or (resid 35...DD14 - 20319 - 208
45GLUGLUMETMET(chain D and (resid 14 through 34 or (resid 35...DD14 - 20319 - 208
46GLUGLUMETMET(chain D and (resid 14 through 34 or (resid 35...DD14 - 20319 - 208

-
Components

#1: Protein
RNA-free ribonuclease P / RNA-free RNase P / Protein-only RNase P


Mass: 23990.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomycetes bacterium GWF2_40_8 (bacteria)
Gene: A2106_02805 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G2XP69, ribonuclease P
#2: RNA chain histidine pre-tRNA


Mass: 27321.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% (v/v) Tacsimate pH 8.0, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 38678 / % possible obs: 99.9 % / Redundancy: 15.1 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.03 / Rrim(I) all: 0.121 / Χ2: 1.019 / Net I/σ(I): 6.9 / Num. measured all: 584223
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.980.59237630.0530.2160.6320.69699.8
2.9-3.029.90.59938080.110.1950.6310.78299.9
3.02-3.1510.80.57838120.1790.1790.6060.751100
3.15-3.3211.30.52938170.3930.160.5540.787100
3.32-3.5313.90.47438400.7380.1280.4920.921100
3.53-3.815.90.35338270.9340.0880.3640.996100
3.8-4.18170.22638670.9680.0560.2331.1299.9
4.18-4.7820.80.11938780.9950.0260.1211.131100
4.78-6.0220.80.08339380.9970.0180.0851.151100
6.02-3021.70.03541280.9980.0080.0361.21699.8

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E8K

7e8k


Resolution: 2.804→29.459 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 1677 4.97 %
Rwork0.2295 32060 -
obs0.2323 33737 87.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.68 Å2 / Biso mean: 65.35 Å2 / Biso min: 12.9 Å2
Refinement stepCycle: final / Resolution: 2.804→29.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 1444 5 9 7605
Biso mean--86.14 36.84 -
Num. residues----827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097855
X-RAY DIFFRACTIONf_angle_d1.60410907
X-RAY DIFFRACTIONf_chiral_restr0.0741317
X-RAY DIFFRACTIONf_plane_restr0.011123
X-RAY DIFFRACTIONf_dihedral_angle_d16.3544705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3512X-RAY DIFFRACTION22.166TORSIONAL
12B3512X-RAY DIFFRACTION22.166TORSIONAL
13C3512X-RAY DIFFRACTION22.166TORSIONAL
14D3512X-RAY DIFFRACTION22.166TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8042-2.88660.28250.35464421
2.8866-2.97970.3686690.3296142847
2.9797-3.08610.38051080.3064248082
3.0861-3.20950.3531480.3025286795
3.2095-3.35540.31461680.2711300599
3.3554-3.5320.31241650.25843023100
3.532-3.75290.31661630.24133034100
3.7529-4.0420.26911580.22343028100
4.042-4.44760.26931780.19663067100
4.4476-5.08830.25231810.17753056100
5.0883-6.39980.25461550.21913140100
6.3998-29.4590.25041590.19443288100
Refinement TLS params.Method: refined / Origin x: -34.8177 Å / Origin y: 17.6368 Å / Origin z: 2.1647 Å
111213212223313233
T0.1247 Å2-0.0504 Å20.0505 Å2-0.1907 Å2-0.2808 Å2--0.1466 Å2
L1.2871 °20.405 °20.1822 °2-1.183 °20.3791 °2--1.7311 °2
S0.3463 Å °0.1293 Å °-0.1376 Å °-0.0933 Å °-0.0561 Å °-0.0846 Å °-0.2952 Å °0.3092 Å °-0.0477 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 203
2X-RAY DIFFRACTION1allB13 - 203
3X-RAY DIFFRACTION1allC10 - 203
4X-RAY DIFFRACTION1allD14 - 203
5X-RAY DIFFRACTION1allX-1 - 72
6X-RAY DIFFRACTION1allM1 - 6
7X-RAY DIFFRACTION1allF1 - 9

+
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