[English] 日本語
Yorodumi
- PDB-5xj2: Structure of spRlmCD with U747 RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xj2
TitleStructure of spRlmCD with U747 RNA
Components
  • RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')
  • Uncharacterized RNA methyltransferase SP_1029
KeywordsTRANSFERASE/RNA / methyltransferase / 23S rRNA / U747 / TRANSFERASE-RNA complex
Function / homology
Function and homology information


: / RNA modification / RNA methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. ...RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Uncharacterized RNA methyltransferase SP_1029
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4TIGR4 (bacteria)
Streptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsJiang, Y. / Gong, Q.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD
Authors: Jiang, Y. / Li, F. / Wu, J. / Shi, Y. / Gong, Q.
History
DepositionApr 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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: Uncharacterized RNA methyltransferase SP_1029
B: Uncharacterized RNA methyltransferase SP_1029
C: Uncharacterized RNA methyltransferase SP_1029
D: Uncharacterized RNA methyltransferase SP_1029
G: RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,15613
Polymers211,3575
Non-polymers1,7998
Water27015
1
A: Uncharacterized RNA methyltransferase SP_1029
G: RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6484
Polymers57,1992
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8363
Polymers51,3861
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8363
Polymers51,3861
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8363
Polymers51,3861
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.384, 94.916, 164.164
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 4511 - 451
21METMETLEULEUBB1 - 4511 - 451
12LEULEULEULEUAA2 - 4512 - 451
22LEULEULEULEUCC2 - 4512 - 451
13LEULEUASPASPAA2 - 4522 - 452
23LEULEUASPASPDD2 - 4522 - 452
14LEULEULEULEUBB2 - 4512 - 451
24LEULEULEULEUCC2 - 4512 - 451
15LEULEULEULEUBB2 - 4512 - 451
25LEULEULEULEUDD2 - 4512 - 451
16LEULEULEULEUCC2 - 4512 - 451
26LEULEULEULEUDD2 - 4512 - 451

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Uncharacterized RNA methyltransferase SP_1029


Mass: 51386.047 Da / Num. of mol.: 4 / Fragment: UNP residues 1-454 / Mutation: E443Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4TIGR4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1029 / Plasmid: pET28aSUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: Q97R12, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')


Mass: 5812.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae TIGR4 (bacteria)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM MES 0.1M ammonium sulfate 0.01 M magnesium chloride 20%PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / Num. obs: 45742 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.366 / Rpim(I) all: 0.18 / Rrim(I) all: 0.409 / Χ2: 0.567 / Net I/σ(I): 2.9 / Num. measured all: 215130
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.94.10.99123260.6140.5251.1260.47899.9
2.9-2.954.31.06522370.6770.5511.2030.47799.7
2.95-3.014.40.99322810.6890.5071.1190.4899.6
3.01-3.074.30.98822530.7270.5051.1130.49499.7
3.07-3.144.30.89422650.7060.4581.0080.49299.7
3.14-3.214.50.86122750.7870.4330.9680.50399.8
3.21-3.294.70.75522850.8520.3710.8430.51799.9
3.29-3.384.50.62422700.860.3140.7010.522100
3.38-3.484.80.56922790.7820.2780.6340.587100
3.48-3.5950.47322690.9490.2250.5240.569100
3.59-3.7250.42722920.9460.2040.4740.61100
3.72-3.8750.40222710.9560.1920.4460.572100
3.87-4.0450.34522770.9660.1650.3830.64599.9
4.04-4.264.90.26623100.9730.1280.2960.60499.9
4.26-4.524.70.2122860.9660.1050.2350.657100
4.52-4.874.80.17922900.9810.0880.20.623100
4.87-5.364.80.19222870.9860.0930.2140.56299.7
5.36-6.135.20.21422970.9830.1010.2370.535100
6.13-7.724.90.17523130.9860.0840.1950.56899.7
7.72-404.70.08923790.9920.0430.0990.778100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWV

1uwv


Resolution: 2.84→39.53 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.1787 / FOM work R set: 0.8292 / SU B: 16.43 / SU ML: 0.307 / SU Rfree: 0.3937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1999 4.4 %RANDOM
Rwork0.1953 ---
obs0.1971 43704 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.4 Å2 / Biso mean: 29.664 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.01 Å2
2---0.04 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.84→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14221 211 108 15 14555
Biso mean--46.33 6.57 -
Num. residues----1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914822
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213916
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9620143
X-RAY DIFFRACTIONr_angle_other_deg1.015332257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33951805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75224.977663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.584152576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4931575
X-RAY DIFFRACTIONr_chiral_restr0.1050.22331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022836
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A274940.1
12B274940.1
21A282700.09
22C282700.09
31A278900.11
32D278900.11
41B274600.11
42C274600.11
51B274520.11
52D274520.11
61C278540.11
62D278540.11
LS refinement shellResolution: 2.84→2.914 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 143 -
Rwork0.279 3115 -
all-3258 -
obs--95.8 %

+
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