[English] 日本語
Yorodumi
- PDB-2g0c: Structure of the RNA binding domain (residues 404-479) of the Bac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g0c
TitleStructure of the RNA binding domain (residues 404-479) of the Bacillus subtilis YxiN protein
ComponentsATP-dependent RNA helicase dbpA
KeywordsHYDROLASE / RNA recognition motif
Function / homology
Function and homology information


RNA strand annealing activity / 3'-5' RNA helicase activity / response to cold / ribosomal large subunit assembly / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase domain ...ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DbpA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsMcKay, D.B.
CitationJournal: RNA / Year: 2006
Title: The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.
Authors: Wang, S. / Hu, Y. / Overgaard, M.T. / Karginov, F.V. / Uhlenbeck, O.C. / McKay, D.B.
History
DepositionFeb 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent RNA helicase dbpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4843
Polymers8,2921
Non-polymers1922
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: ATP-dependent RNA helicase dbpA
hetero molecules

A: ATP-dependent RNA helicase dbpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9686
Polymers16,5842
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1240 Å2
ΔGint-50 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.010, 51.010, 64.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1006-

HOH

21A-1008-

HOH

31A-1025-

HOH

41A-1026-

HOH

-
Components

#1: Protein ATP-dependent RNA helicase dbpA


Mass: 8291.884 Da / Num. of mol.: 1 / Fragment: RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dbpA, deaD / Production host: Escherichia coli (E. coli)
References: UniProt: P42305, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10
Details: precipitant of 3.2-3.6 M (NH4)2SO4 buffered with 0.1 M glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97858, 0.97910, 0.94643
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2004 / Details: wiggler
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978581
20.97911
30.946431
Reflection

D res high: 1.7 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
6.5121.7616200.0512.33944296.9
6.9220.9652490.0421.74951697.2
6.9318.5655140.0461.71953997.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665091884.310.0393.0865.3
2.913.669529510.0392.9626
2.542.919469710.0483.1556.1
2.312.5495598.610.0613.1466.4
2.142.3194698.610.0742.8496.6
2.022.149589910.0892.4416.9
1.912.0295299.410.1251.9757
1.831.9193799.710.1851.5627
1.761.8393899.510.2851.4357
1.71.7694099.810.4131.2437
3.665093785.620.0322.4926
2.913.6696295.620.0322.3546.7
2.542.9195997.320.0432.4226.9
2.312.5495798.720.0512.17
2.142.3194898.920.0621.8327
2.022.1496099.320.0771.5297
1.912.0296399.420.121.3197
1.831.9193799.720.2041.2267
1.761.8395399.520.3251.1477
1.71.7694099.920.4981.1357
3.665095386.830.0332.5146
2.913.6697096.430.0342.3976.7
2.542.9196397.530.0472.4376.9
2.312.5496098.630.0592.0547
2.142.3194598.630.0761.7537
2.022.1495899.130.0981.4237.1
1.912.0296899.230.1611.2747
1.831.9193899.730.2851.1817
1.761.8394699.430.4551.1067
1.71.7693899.730.731.1347
ReflectionResolution: 1.7→50 Å / Num. all: 9484 / Num. obs: 9790 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Χ2: 0.825 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.8 / Num. unique all: 941 / Num. unique obs: 941 / Rsym value: 0.323 / Χ2: 0.659 / % possible all: 99.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SOLVEphasing
RefinementStarting model: de novo

Resolution: 1.7→50 Å / FOM work R set: 0.795 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 579 6.1 %Random
Rwork0.253 ---
all0.253 9484 --
obs0.253 9484 99.2 %-
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 10 48 569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_improper_angle_d1.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.7-1.750.383480.333728776
1.75-1.820.308570.297740797
1.82-1.890.348440.28770814
1.89-1.980.348550.264789844
1.98-2.080.301550.247796851
2.08-2.210.285480.255826874
2.21-2.380.288600.243817877
2.38-2.620.249370.229850887
2.62-30.314620.263838900
3-3.780.229550.234851906
3.78-500.264580.26900958

+
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