[English] 日本語
Yorodumi
- PDB-4p3u: Crystal structure of the bacterial A1408U-mutant ribosomal decodi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p3u
TitleCrystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
Components5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / ribosome / antibiotic-resistance / aminoglycoside / decoding
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKondo, J. / Koganei, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT23790054 Japan
CitationJournal: To Be Published
Title: Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
Authors: Kondo, J. / Koganei, M.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
B: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
C: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
D: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)29,6454
Polymers29,6454
Non-polymers00
Water25214
1
A: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
B: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)14,8232
Polymers14,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area8440 Å2
MethodPISA
2
C: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
D: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)14,8232
Polymers14,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.380, 32.730, 80.990
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: RNA chain
5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Mass: 7411.264 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, PEG3350, Sodium Cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→25.6 Å / Num. obs: 7533 / % possible obs: 99.4 % / Redundancy: 3.53 % / Rmerge(I) obs: 0.091 / Χ2: 0.98 / Net I/σ(I): 7.1 / Num. measured all: 26787 / Scaling rejects: 201
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
3-3.113.570.3772.226357291.1333100
3.11-3.233.590.2422.627327581.151399.9
3.23-3.383.590.1563.326877451.0613100
3.38-3.563.610.1813.426797391.06899.9
3.56-3.783.580.1264.326877460.941599.9
3.78-4.073.560.1115.727157560.962099.9
4.07-4.483.530.106726857550.921799.9
4.48-5.123.540.0888.127187640.8415100
5.12-6.433.510.06911.827247710.811699.9
6.43-25.63.210.03724.325257700.985195.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
PDB_EXTRACT3.14data extraction
MOLREPphasing
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→100 Å / FOM work R set: 0.6361 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3024 808 10.6 %
Rwork0.2951 6724 -
obs-7532 99.2 %
Solvent computationBsol: 69.0349 Å2
Displacement parametersBiso max: 224.93 Å2 / Biso mean: 142.0724 Å2 / Biso min: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1--23.491 Å20 Å254.464 Å2
2---1.739 Å20 Å2
3---25.231 Å2
Refinement stepCycle: final / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1832 0 14 1846
Biso mean---80.9 -
Num. residues----86
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.287
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.2822
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.112.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.5907790.6207649X-RAY DIFFRACTION100
3.11-3.230.6184770.53687X-RAY DIFFRACTION99.9
3.23-3.380.5075800.4564662X-RAY DIFFRACTION100
3.56-3.780.3538790.4021662X-RAY DIFFRACTION99.9
3.78-4.070.369840.3543666X-RAY DIFFRACTION99.9
4.07-4.480.2625830.28671X-RAY DIFFRACTION99.9
4.48-5.130.2367780.2495677X-RAY DIFFRACTION99.9
5.13-6.460.2737890.2367675X-RAY DIFFRACTION99.9
6.46-25.60.2143770.1965702X-RAY DIFFRACTION99.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1bru.param
X-RAY DIFFRACTION2dna-rna_free.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

+
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