[English] 日本語
Yorodumi
- PDB-4y1i: Lactococcus lactis yybP-ykoY Mn riboswitch bound to Mn2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y1i
TitleLactococcus lactis yybP-ykoY Mn riboswitch bound to Mn2+
ComponentsLactococcus lactis yybP-ykoY riboswitch
KeywordsRNA / riboswitch / manganese-binding
Function / homology: / GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsPrice, I.R. / Ke, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086766 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 102543 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.
Authors: Price, I.R. / Gaballa, A. / Ding, F. / Helmann, J.D. / Ke, A.
History
DepositionFeb 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactococcus lactis yybP-ykoY riboswitch
B: Lactococcus lactis yybP-ykoY riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,03751
Polymers64,6092
Non-polymers4,42849
Water1,00956
1
A: Lactococcus lactis yybP-ykoY riboswitch
B: Lactococcus lactis yybP-ykoY riboswitch
hetero molecules

A: Lactococcus lactis yybP-ykoY riboswitch
B: Lactococcus lactis yybP-ykoY riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,073102
Polymers129,2174
Non-polymers8,85698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18200 Å2
ΔGint-752 kcal/mol
Surface area63730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.285, 127.881, 115.324
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
RNA chain , 1 types, 2 molecules AB

#1: RNA chain Lactococcus lactis yybP-ykoY riboswitch


Mass: 32304.258 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Lactococcus lactis subsp. lactis (lactic acid bacteria)

-
Non-polymers , 5 types, 105 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ba
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: RNA solution: 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, 2.5 mM MnCl2, Mother liquor: 14% (+/-)-2-methyl-2,4-pentanediol (MPD) , 40 mM Na cacodylate pH 7.0, 80 mM NaCl, 20 mM BaCl2, ...Details: RNA solution: 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, 2.5 mM MnCl2, Mother liquor: 14% (+/-)-2-methyl-2,4-pentanediol (MPD) , 40 mM Na cacodylate pH 7.0, 80 mM NaCl, 20 mM BaCl2, 12 mM spermine tetra-HCl, at 21 C, with 1:2 RNA: mother liquor drop ratio. Cryoprotection: 20% PEG-400 and 0.1 mM MnCl2 overnight soak.

-
Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.892 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.892 Å / Relative weight: 1
ReflectionResolution: 2.85→55.9 Å / Num. obs: 20952 / % possible obs: 92 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 20.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.87 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1834)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphenix.autosolphasing
RefinementResolution: 2.85→55.9 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 2125 9.74 %
Rwork0.1928 --
obs0.1957 19804 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4284 111 56 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134925
X-RAY DIFFRACTIONf_angle_d0.4257584
X-RAY DIFFRACTIONf_dihedral_angle_d15.8442470
X-RAY DIFFRACTIONf_chiral_restr0.0181000
X-RAY DIFFRACTIONf_plane_restr0.002202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.88480.48311560.46321265X-RAY DIFFRACTION88
2.8848-2.92130.44591320.41971306X-RAY DIFFRACTION89
2.9213-2.95970.40151370.38181251X-RAY DIFFRACTION89
2.9597-3.00030.36681640.32531330X-RAY DIFFRACTION90
3.0003-3.04310.32851360.2871279X-RAY DIFFRACTION89
3.0431-3.08850.32641230.27411272X-RAY DIFFRACTION89
3.0885-3.13680.33111490.28881295X-RAY DIFFRACTION87
3.1368-3.18820.30791040.27051261X-RAY DIFFRACTION87
3.1882-3.24320.28551550.23541161X-RAY DIFFRACTION83
3.2432-3.30220.23531240.21711192X-RAY DIFFRACTION80
3.3022-3.36570.24041190.23741331X-RAY DIFFRACTION92
3.3657-3.43440.21031620.20921300X-RAY DIFFRACTION91
3.4344-3.5090.21411540.21581299X-RAY DIFFRACTION92
3.509-3.59070.20381510.21341324X-RAY DIFFRACTION91
3.5907-3.68040.24931250.20841278X-RAY DIFFRACTION90
3.6804-3.77990.23441550.19731328X-RAY DIFFRACTION91
3.7799-3.89110.23061280.19071261X-RAY DIFFRACTION89
3.8911-4.01670.1871350.17621337X-RAY DIFFRACTION89
4.0167-4.16020.1761380.16771157X-RAY DIFFRACTION82
4.1602-4.32680.15151450.15911338X-RAY DIFFRACTION93
4.3268-4.52360.2271470.15511382X-RAY DIFFRACTION94
4.5236-4.7620.2031430.16641352X-RAY DIFFRACTION93
4.762-5.06020.16451360.15941337X-RAY DIFFRACTION94
5.0602-5.45070.20931410.15791323X-RAY DIFFRACTION92
5.4507-5.99870.21141330.15791247X-RAY DIFFRACTION84
5.9987-6.86570.23381540.18211353X-RAY DIFFRACTION95
6.8657-8.64580.18691420.16771372X-RAY DIFFRACTION94
8.6458-59.47810.20551280.15951340X-RAY DIFFRACTION91

+
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