[English] 日本語
Yorodumi
- PDB-6ymm: Crystal structure of the SAM-SAH riboswitch with SAM from space g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ymm
TitleCrystal structure of the SAM-SAH riboswitch with SAM from space group P312
Components
  • Chains: A
  • Chains: B,D
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyS-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
Ministry of Education (MoE, China) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.
Authors: Huang, L. / Liao, T.W. / Wang, J. / Ha, T. / Lilley, D.M.J.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chains: A
B: Chains: B,D
C: Chains: A
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7908
Polymers22,5714
Non-polymers1,2184
Water19811
1
A: Chains: A
B: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1065
Polymers11,2862
Non-polymers8203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chains: A
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6843
Polymers11,2862
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.170, 88.170, 76.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: -y,-x,-z
#5: -x+y,y,-z
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

-
Components

#1: RNA chain Chains: A


Mass: 8389.874 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#2: RNA chain Chains: B,D


Mass: 2895.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9198 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.2→76.08 Å / Num. obs: 32912 / % possible obs: 99.6 % / Redundancy: 14.2 % / Biso Wilson estimate: 61.11 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.022 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 801 / CC1/2: 0.696 / Rpim(I) all: 0.52 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.18 Å / SU ML: 0.4099 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.4545
RfactorNum. reflection% reflection
Rfree0.2211 1688 5.13 %
Rwork0.1923 --
obs0.1939 32912 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1484 67 11 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761728
X-RAY DIFFRACTIONf_angle_d1.63952681
X-RAY DIFFRACTIONf_chiral_restr0.1223356
X-RAY DIFFRACTIONf_plane_restr0.010173
X-RAY DIFFRACTIONf_dihedral_angle_d17.0192857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.38241150.43522402X-RAY DIFFRACTION91.33
2.26-2.340.44051060.40712568X-RAY DIFFRACTION95.5
2.34-2.420.45741760.37642518X-RAY DIFFRACTION96.32
2.42-2.520.35841400.36772571X-RAY DIFFRACTION96.75
2.52-2.630.39571270.34692633X-RAY DIFFRACTION98.05
2.63-2.770.41441350.32082620X-RAY DIFFRACTION98.96
2.77-2.950.3451210.30472669X-RAY DIFFRACTION99.32
2.95-3.170.25561420.22982647X-RAY DIFFRACTION99.79
3.17-3.490.21491640.1842632X-RAY DIFFRACTION99.96
3.49-40.22251570.16942666X-RAY DIFFRACTION99.93
4-5.030.17361350.14042647X-RAY DIFFRACTION100
5.03-38.180.14131700.1292651X-RAY DIFFRACTION99.79
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)
15.396046680114.02334299953.370716005856.32173626566-0.8905382127195.87801855942-0.6606009034730.637729361803-1.1266042779-0.1067603455270.312547471305-0.5477683526140.1170536853360.5013468570480.2985170445110.653681057136-0.01506979053330.1042889673560.693602185426-0.05052136391360.59009111013523.1870454325-11.102514073726.1683361559
25.139339560570.790347833401-0.9418037360531.27903084366-0.1852095093740.8151181907530.04071350392330.1088700448040.0552266128765-0.1131003638750.05654876696140.00658991256924-0.1191998461920.0241220342388-0.1310167426980.645942354563-0.0332189115193-0.01141731163920.633069229274-0.05040771677080.5006350619293.51946956502-14.394430051224.8616472359
38.485904942383.996502901884.788708409736.037346745821.598982297784.05516333377-0.350775723321-0.39584883528-0.0516253889525-0.1265807958960.268155449982-0.5500697435360.1188792384890.2788022032210.006384924891720.6675118986370.003067974120120.1440610826290.798991654934-0.107719032140.66181068443623.7756047013-5.6280867558220.5292256215
42.68849009678-1.91730272839-0.7275958725541.37205447217-0.07348856178382.00139133570.2036026098240.435683481839-0.303113655416-0.019411686631-0.2861275345190.0628771983306-0.00578622581382-0.1478748828870.1294167687280.599436846414-0.0275382468446-0.06227614989680.697909994508-0.03569847541840.555744253362-2.92328997352-22.64246279128.2094719207
57.835786798894.20653864991-6.023655083094.82429692616-2.414602897024.87667625724-0.7078554252310.323137945836-0.718143224601-0.639123822748-0.1933798942510.4608706517920.510494427624-0.2435053660850.836828347540.689734937278-0.11327468503-0.0590912916621.03417247460.01815622708920.97931075979347.8961670681-3.0005098088511.5796008234
64.545631509092.70545049426-3.107452252747.61615814381-0.6753314437912.05489733452-0.7858822102340.721798645067-0.257211599312-0.6708671299640.4719083410090.9774389262640.64563880187-0.6283685202610.3900304480470.795514544322-0.165756555309-0.08927366354731.024215330730.03954392536330.80327903350949.1685823636-2.8481388126810.8928273264
72.251585496923.411981312980.7590044282459.28663784995-1.602811202054.14278543316-0.3724253750420.8775334767010.273375577271-0.5292020970020.3662885693490.97254800985-0.486967022971-0.6859577004570.03486594480780.6602725404730.00401971354982-0.09322166936950.8156518461660.04584078952230.590381475658.150159046811.756862308110.8390224083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 32 )
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 51 )
5X-RAY DIFFRACTION5chain 'C' and (resid 7 through 17 )
6X-RAY DIFFRACTION6chain 'C' and (resid 18 through 32 )
7X-RAY DIFFRACTION7chain 'D' and (resid 43 through 51 )

+
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