[English] 日本語
Yorodumi
- PDB-1tyh: Crystal Structure of Transcriptional Activator tenA from Bacillus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tyh
TitleCrystal Structure of Transcriptional Activator tenA from Bacillus subtilis
ComponentsTranscriptional activator tenA
KeywordsTRANSCRIPTION / all helical structure / tetramer / tenA / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytosol
Similarity search - Function
Thiaminase II / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Transcriptional Activator tenA from Bacillus subtilis
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionJul 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional activator tenA
B: Transcriptional activator tenA
D: Transcriptional activator tenA
E: Transcriptional activator tenA


Theoretical massNumber of molelcules
Total (without water)116,3534
Polymers116,3534
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-49 kcal/mol
Surface area34630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.430, 58.430, 297.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein
Transcriptional activator tenA


Mass: 29088.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: TENA, BSU11650 / Production host: Escherichia coli (E. coli) / References: UniProt: P25052
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: PEG 4000, Sodium Citrate, Glycerol, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97959, 0.97991, 0.94
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2004 / Details: Si Mirrors
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979591
20.979911
30.941
ReflectionResolution: 2.53→50 Å / Num. all: 32993 / Num. obs: 32993 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.401 / Num. unique all: 3194 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.54→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A continuous electron density appears between residues ASP 44 and CYS 135. This density might represent either a possible cofactor or a substrate which is unknown at this time and not ...Details: A continuous electron density appears between residues ASP 44 and CYS 135. This density might represent either a possible cofactor or a substrate which is unknown at this time and not modeled. Instead, the density is modeled with discrete water molecules (1, 2, 11, 18, 35, 73, 111, 112 and 113).
RfactorNum. reflection% reflectionSelection details
Rfree0.3039 1572 -RANDOM
Rwork0.2437 ---
obs0.2437 31624 96.9 %-
all-31624 --
Refinement stepCycle: LAST / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7140 0 0 112 7252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.235
X-RAY DIFFRACTIONc_bond_d0.0086

+
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