[English] 日本語
Yorodumi
- PDB-5fk5: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is AA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fk5
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is AA
ComponentsSAM-I RIBOSWITCH
KeywordsRNA / KINK TURN / RNA MOTIF / SAM-I RIBOSWITCH
Function / homology: / : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesTHERMOANAEROBACTER TENGCONGENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.315 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function.
Authors: Huang, L. / Wang, J. / Lilley, D.M.J.
History
DepositionOct 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _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: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,71616
Polymers30,5911
Non-polymers2,12515
Water00
1
A: SAM-I RIBOSWITCH
hetero molecules

A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,43232
Polymers61,1832
Non-polymers4,24930
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7500 Å2
ΔGint-258 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.784, 61.784, 154.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1125-

BA

-
Components

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30591.377 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN, RESIDUES 1-93 / Source method: obtained synthetically
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.62 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 15 MM BACL2, 12 MM SPERMINE-HCL, 8% (V/V) MPD

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.31→28.99 Å / Num. obs: 4912 / % possible obs: 99.8 % / Observed criterion σ(I): 2.7 / Redundancy: 9.2 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.9
Reflection shellResolution: 3.31→3.4 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2.9 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FJC

5fjc


Resolution: 3.315→28.988 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 838 9.9 %
Rwork0.199 --
obs0.2043 4859 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.75 Å2
Refinement stepCycle: LAST / Resolution: 3.315→28.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2032 41 0 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032308
X-RAY DIFFRACTIONf_angle_d0.7183599
X-RAY DIFFRACTIONf_dihedral_angle_d16.7151139
X-RAY DIFFRACTIONf_chiral_restr0.037475
X-RAY DIFFRACTIONf_plane_restr0.00596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3147-3.5220.37271290.32061259X-RAY DIFFRACTION99
3.522-3.79340.29251460.25761270X-RAY DIFFRACTION100
3.7934-4.17420.32511460.22331276X-RAY DIFFRACTION99
4.1742-4.77580.25291370.19541273X-RAY DIFFRACTION100
4.7758-6.00820.23291370.1661266X-RAY DIFFRACTION100
6.0082-28.98870.19331430.16911282X-RAY DIFFRACTION100
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)
16.90032.2171-4.78582.5177-3.57156.8933-0.44260.35670.2587-1.3265-0.04860.1115-1.02971.00690.24991.2433-0.4079-0.18680.86670.06710.99670.7807-13.701938.1154
22.97040.44543.01476.3799-0.06563.1042-0.77150.0244-1.2666-0.2423-0.49160.40860.170.21790.94130.7364-0.3039-0.04061.2236-0.03160.7747-14.1091-14.267834.8915
32.90240.45760.39383.433-1.7623.45230.37110.4213-0.2431-0.18960.0725-0.56931.5170.2321-0.46751.1780.2213-0.47021.4213-0.39181.0555-21.4422-7.718121.0256
40.66870.9776-0.42781.5831-0.26840.9108-0.25980.37231.1257-1.4517-0.3385-0.23050.3072-1.12660.3182.41140.1076-0.09472.56480.85071.8813-14.48389.1211.0074
57.8041-1.2406-3.53643.55570.48072.13420.3060.11121.7245-0.75621.0595-0.5196-1.92770.598-1.0582.7303-0.42080.19250.9365-0.11461.0162-0.55867.37838.004
60.2014-0.5696-0.15931.69820.4680.1299-0.055-0.05950.0294-0.1027-0.0154-0.032-0.710.1256-0.36050.8790.0789-0.00841.2484-1.35341.7099-1.7972-9.161513.3584
70.52-0.02590.64820.3005-0.20260.9136-0.14630.5269-0.25-0.38510.1389-0.64450.47840.3021-0.03881.05840.53450.42092.0003-0.93761.0828-1.3854-20.315512.953
80.90460.5161-0.51661.5593-0.77180.4791-0.15380.064-0.119-0.5392-0.4263-0.4340.4022-0.16920.11391.11460.01810.26161.8106-0.64961.0541-7.1112-8.7184.3991
96.2308-0.95674.77533.6704-2.73854.8286-0.4888-0.2962-0.45970.126-0.33080.7952-0.3713-0.98690.78991.3061-0.03990.14051.1667-0.49881.0685-4.97582.82649.7686
103.70630.8861-2.33923.3623-2.75133.20290.02-0.39570.192-1.08950.18750.8522-1.00830.3064-0.25051.55170.3528-0.27531.1767-0.20280.739-15.70457.292322.4651
112.7864-2.96830.43674.3846-1.64771.3677-0.1704-0.6393-0.4362-0.238-0.0590.52790.1566-0.12810.23910.61910.09020.07911.231-0.14060.5738-17.2010.018837.7004
123.4937-1.8187-1.96431.15431.22461.2661-1.0575-0.229-0.48071.27110.31930.6025-0.6146-1.31080.55181.20780.30930.21552.0253-0.09810.897-18.70769.726639.5205
138.0233-2.0521-6.526.41922.06185.32410.0099-0.29940.5368-0.3252-0.26560.12290.0524-0.13850.0920.92740.05840.10711.3085-0.22220.5854-11.08590.05726.1778
140.5410.543-0.65640.5757-0.50451.621-0.0972-0.1295-0.1291-0.086-0.25360.3382-0.14430.16510.01061.1889-0.6807-0.40041.4731-0.5755-0.0765-14.8974-11.784816.268
156.9481-0.5407-1.01871.77662.56943.71990.7555-0.1191-0.03980.96990.4894-0.73260.70691.1735-0.91.058-0.0668-0.12831.4378-0.29991.0305-8.3441-23.068717.9402
163.1815-0.86742.40410.3042-1.07954.431-0.3117-0.08290.31070.1705-0.4092-0.37110.14540.3077-0.1772.81720.1267-1.00061.09870.34081.083-14.5499-37.382523.4876
170.4958-0.3031-0.42232.37841.05850.62761.19120.2918-1.01620.03880.1114-0.07020.70850.0653-0.89561.68360.2392-0.40870.73530.07290.8755-17.4871-36.455613.2371
180.41390.0703-0.05070.8651-0.5620.92090.11270.0444-0.09360.13470.4460.1738-0.19110.2638-0.34631.9250.0844-0.010.8105-0.16431.0713-12.5886-26.718828.0615
194.897-0.36-0.37132.258-1.18955.12720.8863-0.014-1.25130.8022-0.35260.03781.12250.621-0.75330.5825-0.116-0.23850.7821-0.00430.7652-6.8089-11.091931.3707
200.09130.241-0.54292.0941-0.02274.5049-0.55480.3344-0.0934-0.3732-0.1113-0.15-1.33490.66380.34130.6687-0.4701-0.70941.38740.2861-0.03190.6969-8.42944.9874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:8)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 9:12)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 13:16)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 17:20)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 21:24)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 25:28)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 29:33)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 34:39)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 40:45)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 46:49)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 50:56)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 57:60)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 61:64)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 65:69)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 70:73)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 74:80)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 81:84)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 85:90)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 91:94)

+
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