[English] 日本語
Yorodumi
- PDB-3dim: Crystallization of the Thermotoga maritima lysine riboswitch boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dim
TitleCrystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Cs+ Soak
ComponentsRNA (174-MER)
KeywordsRNA / riboswitch / lysine
Function / homology: / ISOPROPYL ALCOHOL / LYSINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSerganov, A.A.
CitationJournal: Nature / Year: 2008
Title: Structural insights into amino acid binding and gene control by a lysine riboswitch.
Authors: Serganov, A. / Huang, L. / Patel, D.J.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_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: RNA (174-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,69221
Polymers56,6361
Non-polymers1,05620
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.249, 79.043, 141.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (174-MER)


Mass: 56635.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Thermotoga maritima MSB8 asd gene

-
Non-polymers , 6 types, 46 molecules

#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 18% PEG4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2Sodium Citrate11
3isopropanol11
4PEG400012
5Sodium Citrate12
6isopropanol12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.84 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.84 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 14119 / Num. obs: 13695 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 2.9→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1401 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3DIL

3dil


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.897 / SU B: 34.675 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: tls / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24778 680 5 %RANDOM
Rwork0.20308 ---
all0.20525 13369 --
obs0.20525 12788 95.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---3.46 Å20 Å2
3---2.76 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3752 34 26 3812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214214
X-RAY DIFFRACTIONr_angle_refined_deg1.2932.9996572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.326154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021838
X-RAY DIFFRACTIONr_nbd_refined0.1720.21608
X-RAY DIFFRACTIONr_nbtor_refined0.2690.22623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2136
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.29
X-RAY DIFFRACTIONr_mcbond_it0.2171.57
X-RAY DIFFRACTIONr_mcangle_it0.38728
X-RAY DIFFRACTIONr_scbond_it0.5934307
X-RAY DIFFRACTIONr_scangle_it0.9394.56564
LS refinement shellResolution: 2.9→2.974 Å / Rfactor Rfree error: 0.408 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 48 -
Rwork0.319 918 -
obs-1005 96.12 %
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)
10.7552-0.2444-0.21762.2152-0.52672.22-0.02260.2042-0.2012-0.34850.13560.0640.4778-0.251-0.11290.06050.0094-0.0276-0.16840.00550.136929.683-1.85718.901
21.0814-0.21820.45530.37740.09910.9749-0.08540.15720.4018-0.0713-0.0639-0.0073-0.444-0.24030.14930.14760.0966-0.0136-0.08890.03890.28947.25347.28621.119
33.9282-1.630.91380.89840.03711.04130.08670.1066-0.0281-0.1652-0.08120.1678-0.1730.0084-0.00550.01740.0355-0.0238-0.1448-0.01950.12058.78527.19511.2
44.6087-2.00990.49240.878-0.23480.33210.14370.64020.5661-0.0926-0.276-0.3856-0.16880.06920.13230.03360.0309-0.0088-0.15810.06750.209929.84433.65915.313
55.2013-0.1708-0.62041.76720.38070.7883-0.2001-0.1306-0.67610.33790.02-0.2820.1890.14460.1801-0.00420.025-0.004-0.04960.07410.365750.4358.65115.906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 111 - 11
2X-RAY DIFFRACTION1AA163 - 174163 - 174
3X-RAY DIFFRACTION2AA12 - 7912 - 79
4X-RAY DIFFRACTION3AA80 - 11380 - 113
5X-RAY DIFFRACTION4AA114 - 140114 - 140
6X-RAY DIFFRACTION5AA141 - 162141 - 162

+
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