[English] 日本語
Yorodumi
- PDB-3rio: Crystal structure of GlcT CAT-PRDI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rio
TitleCrystal structure of GlcT CAT-PRDI
ComponentsPtsGHI operon antiterminator
KeywordsTRANSCRIPTION / twisted beta sheet / four helix bundle / transcriptional antitermination
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / RNA binding
Similarity search - Function
Transcription Regulation, Sacy; Chain A / CAT RNA-binding domain / PRD domain / PTS-regulatory domain, PRD / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain ...Transcription Regulation, Sacy; Chain A / CAT RNA-binding domain / PRD domain / PTS-regulatory domain, PRD / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PtsGHI operon antiterminator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsHimmel, S. / Grosse, C. / Wolff, S. / Becker, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the RBD-PRDI fragment of the antiterminator protein GlcT.
Authors: Himmel, S. / Grosse, C. / Wolff, S. / Schwiegk, C. / Becker, S.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PtsGHI operon antiterminator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1917
Polymers20,6391
Non-polymers5536
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.755, 47.597, 126.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PtsGHI operon antiterminator / RNA-binding antitermination protein GlcT


Mass: 20638.682 Da / Num. of mol.: 1
Fragment: Co-Antiterminator domain and Phosphoenolpyruvate - phoshphotransferase system domain 1, residues 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU13880, glcT, ykwA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31691
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Na formate, PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.999
SYNCHROTRONSLS X10SA20.9792, 0.9794, 0.9715
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELNov 27, 2010Si(111) monochromator
DECTRIS PILATUS 6M2PIXELNov 27, 2010Si(111) monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9991
20.97921
30.97941
40.97151
ReflectionResolution: 1.99→63.39 Å / Num. all: 15190 / Num. obs: 15190 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.89 Å2
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.15 % / % possible all: 97.1

-
Processing

Software
NameVersionClassification
SHELXDphasing
BUSTER2.8.0refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.99→63.39 Å / Cor.coef. Fo:Fc: 0.8981 / Cor.coef. Fo:Fc free: 0.8797 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 760 5 %RANDOM
Rwork0.21 ---
all0.2118 15190 --
obs0.2118 15190 --
Displacement parametersBiso mean: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.3241 Å20 Å20 Å2
2---15.735 Å20 Å2
3---13.4109 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 1.99→63.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 36 135 1490
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011381HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.121857HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d486SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes194HARMONIC5
X-RAY DIFFRACTIONt_it1381HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion17.51
X-RAY DIFFRACTIONt_chiral_improper_torsion182SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1743SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.13 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2465 140 5.48 %
Rwork0.21 2414 -
all0.2244 2554 -

+
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