[English] 日本語
Yorodumi
- PDB-1rtw: X-ray Structure of PF1337, a TenA Homologue from Pyrococcus furio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rtw
TitleX-ray Structure of PF1337, a TenA Homologue from Pyrococcus furiosus. Northeast Structural Genomics Research Consortium (Nesg) Target PFR34
Componentstranscriptional activator, putativeActivator (genetics)
Keywordsstructural genomics / unknown function / pf1337 / tena / thiamin / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


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
Chem-MP5 / PHOSPHATE ION / Transcriptional activator, putative
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsBenach, J. / Edstrom, W.C. / Lee, I. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.
Authors: Benach, J. / Edstrom, W.C. / Lee, I. / Das, K. / Cooper, B. / Xiao, R. / Liu, J. / Rost, B. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Remark 600ligand THE NATURE OF THE LIGAND IS TENTATIVE. THE LIGAND MP5 IS IS CLEARLY VISIBLE ONLY IN MONOMER ...ligand THE NATURE OF THE LIGAND IS TENTATIVE. THE LIGAND MP5 IS IS CLEARLY VISIBLE ONLY IN MONOMER A. IN THE OTHER MONOMERS, ONLY THE PHOSPHATE PART OF THE LIGAND HAS BEEN MODELLED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: transcriptional activator, putative
B: transcriptional activator, putative
C: transcriptional activator, putative
D: transcriptional activator, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5518
Polymers107,0474
Non-polymers5044
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-68 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.8, 123.65, 77.47
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
transcriptional activator, putative / Activator (genetics)


Mass: 26761.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Plasmid: pET21d / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) containing rare-tRNA expression plasmid pMGK
References: UniProt: Q8U189
#2: Chemical ChemComp-MP5 / (4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL DIHYDROGEN PHOSPHATE / 4-Amino-5-hydroxymethyl-2-methylpyrimidine


Mass: 219.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O4P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG400, 200mM CaCl2, 50mM cacodylic acid, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %PEG4001reservoir
2200 mM1reservoirCaCl2
31 mMdithiothreitol1reservoir
450 mMcacodylate1reservoirpH7.5
58 mg/mlprotein1drop
610 mMTris1drop
7100 mM1dropNaCl
85 mMdithiothreitol1droppH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979, 0.9794, 0.95
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 12, 2003
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.951
ReflectionResolution: 2.35→100 Å / Num. obs: 40075 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.7
Reflection shellResolution: 2.35→2.38 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 73637 / % possible obs: 93.5 % / Redundancy: 3.3 % / Num. measured all: 239958 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Lowest resolution: 2.43 Å / % possible obs: 89.7 % / Redundancy: 3.3 % / Num. unique obs: 6861 / Num. measured obs: 22349 / Rmerge(I) obs: 0.33

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.281 2003
Rwork0.24 -
obs-40075
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7085 0 29 234 7348
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.007
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.1
LS refinement shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.43 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.27

+
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