[English] 日本語
Yorodumi
- PDB-1wol: Crystal Structure of ST0689, an archaeal HEPN homologue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wol
TitleCrystal Structure of ST0689, an archaeal HEPN homologue
Components122aa long conserved hypothetical protein
KeywordsUNKNOWN FUNCTION / ALPHA HELIX / LOOP
Function / homology
Function and homology information


HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TERTIARY-BUTYL ALCOHOL / HEPN domain-containing protein
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsArakawa, T. / Akutsu, J. / Yohda, M.
CitationJournal: To be Published
Title: Crystal Structure Analysis of ST0689, an archaeal HEPN protein
Authors: Arakawa, T. / Akutsu, J. / Yohda, M.
History
DepositionAug 20, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 122aa long conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3313
Polymers14,1831
Non-polymers1482
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.553, 62.553, 64.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly seems to be a monomer

-
Components

#1: Protein 122aa long conserved hypothetical protein / ST0689


Mass: 14183.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): B834, BL21(DE3) / References: UniProt: Q974G3
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: tert-butanol, citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9765, 0.97894, 0.97924
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2004
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97651
20.978941
30.979241
ReflectionResolution: 1.62→50 Å / Biso Wilson estimate: 22.2 Å2
Reflection shellResolution: 1.62→1.68 Å / Rsym value: 0.177 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→41.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 335259.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3400 9.7 %RANDOM
Rwork0.187 ---
obs0.187 35163 98.6 %-
all-35646 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.7591 Å2 / ksol: 0.378148 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.62 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.62→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 10 84 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.041
X-RAY DIFFRACTIONc_angle_deg3.6
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d3.02
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it3.012
X-RAY DIFFRACTIONc_scbond_it2.782
X-RAY DIFFRACTIONc_scangle_it42.5
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 555 9.7 %
Rwork0.209 5176 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3T-BUTANOL.PARAMT-BUTANOL.TOP

+
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