[English] 日本語
Yorodumi
- PDB-7cf7: Crystal Structure of YbeA CP74 W72F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cf7
TitleCrystal Structure of YbeA CP74 W72F
ComponentsRibosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H
KeywordsTRANSFERASE / YbeA
Function / homology
Function and homology information


23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / rRNA base methylation / rRNA methylation / ribosome binding / protein homodimerization activity / cytoplasm
Similarity search - Function
RNA methyltransferase RlmH / Predicted SPOUT methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6178 Å
AuthorsLiu, C.Y. / Lai, C.H. / Hsu, S.T.D. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal Structure of YbeA CP74 W72F
Authors: Liu, C.Y. / Lai, C.H. / Hsu, S.T.D. / Lyu, P.C.
History
DepositionJun 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H
B: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H


Theoretical massNumber of molelcules
Total (without water)35,2032
Polymers35,2032
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-65 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.628, 38.698, 52.325
Angle α, β, γ (deg.)75.290, 73.800, 76.470
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H / / 23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA ...23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase RlmH


Mass: 17601.389 Da / Num. of mol.: 2 / Mutation: W144F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rlmH, ybeA, b0636, JW0631 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8I8, 23S rRNA (pseudouridine1915-N3)-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Sodium cacodylate pH 6.5, 25% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.6178→30 Å / Num. obs: 32081 / % possible obs: 93.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.042 / Rrim(I) all: 0.069 / Χ2: 1.021 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.682.40.38531440.8320.2980.4891.02692.7
1.68-1.752.70.36831990.8550.2650.4551.02393.7
1.75-1.822.90.27632200.9230.1910.3371.0494.2
1.82-1.922.90.18432400.9580.1270.2241.02194.9
1.92-2.042.90.12832670.980.090.1571.02894.5
2.04-2.22.80.0932130.9870.0650.1111.0494.5
2.2-2.422.70.06632340.9920.0480.0821.00994.6
2.42-2.772.70.05432230.9940.0390.0671.00294.2
2.77-3.492.60.03931220.9960.030.051.00491.2
3.49-302.20.02532190.9970.0240.0351.00694.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.62 Å23.61 Å
Translation1.62 Å23.61 Å

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYO

5zyo


Resolution: 1.6178→23.6084 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1985 6.19 %
Rwork0.1885 30094 -
obs0.1904 32079 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.21 Å2 / Biso mean: 24.4798 Å2 / Biso min: 9.35 Å2
Refinement stepCycle: final / Resolution: 1.6178→23.6084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 0 265 2494
Biso mean---31.13 -
Num. residues----291
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6178-1.65820.28011290.2361185783
1.6582-1.7030.26941280.2204220194
1.703-1.75310.27541560.2181216494
1.7531-1.80970.24961390.2016217794
1.8097-1.87440.22351440.1975218395
1.8744-1.94940.22381410.1982218895
1.9494-2.03810.23321480.1849216195
2.0381-2.14540.2061450.1802219194
2.1454-2.27980.23021450.1834218895
2.2798-2.45560.22471410.1951217594
2.4556-2.70240.22931460.2032216494
2.7024-3.09270.24781400.2036215693
3.0927-3.89360.20691350.1772211491
3.8936-23.60840.17871480.1689217595

+
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