[English] 日本語
Yorodumi
- PDB-5gus: Crystal structure of ASCH domain from Zymomonas mobilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gus
TitleCrystal structure of ASCH domain from Zymomonas mobilis
ComponentsHelix-turn-helix domain-containing protein
KeywordsHYDROLASE / nuclease
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
ASCH domain / ASCH domain / PUA-like superfamily
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / ASCH domain-containing ribonuclease
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.951 Å
AuthorsHa, S.C. / Park, S.Y. / Kim, J.S.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA.
Authors: Kim, B.N. / Shin, M. / Ha, S.C. / Park, S.Y. / Seo, P.W. / Hofmann, A. / Kim, J.S.
History
DepositionAug 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Helix-turn-helix domain-containing protein
B: Helix-turn-helix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2599
Polymers34,4942
Non-polymers7657
Water5,314295
1
A: Helix-turn-helix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8806
Polymers17,2471
Non-polymers6335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area8190 Å2
MethodPISA
2
B: Helix-turn-helix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3783
Polymers17,2471
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.999, 51.999, 207.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-420-

HOH

-
Components

#1: Protein Helix-turn-helix domain-containing protein / ASCH domain-containing protein


Mass: 17246.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1) (bacteria)
Strain: ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1
Gene: Zmob_0380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3G0N3
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 40% (w/v) polyethylene glycol 400, 0.1M cacodylic acid (pH 6.5), 0.2M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.951→44 Å / Num. obs: 24746 / % possible obs: 99.9 % / Redundancy: 8.5 % / Net I/σ(I): 22.5
Reflection shellResolution: 1.951→1.98 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 5 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.951→44 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.67
RfactorNum. reflection% reflection
Rfree0.197 1253 5.06 %
Rwork0.1519 --
obs0.1542 24746 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.951→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 43 295 2701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192469
X-RAY DIFFRACTIONf_angle_d1.813345
X-RAY DIFFRACTIONf_dihedral_angle_d16.302950
X-RAY DIFFRACTIONf_chiral_restr0.14363
X-RAY DIFFRACTIONf_plane_restr0.01421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9505-2.02860.21281350.15072534X-RAY DIFFRACTION100
2.0286-2.12090.20171360.1532561X-RAY DIFFRACTION100
2.1209-2.23280.22231360.14342560X-RAY DIFFRACTION100
2.2328-2.37260.21331400.14752603X-RAY DIFFRACTION100
2.3726-2.55580.21021360.15952544X-RAY DIFFRACTION100
2.5558-2.8130.19961390.16532600X-RAY DIFFRACTION100
2.813-3.21990.23591360.16052641X-RAY DIFFRACTION100
3.2199-4.05630.18421410.13632643X-RAY DIFFRACTION100
4.0563-44.0180.16071540.15572807X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -38.5931 Å / Origin y: 17.4686 Å / Origin z: 18.9942 Å
111213212223313233
T0.1788 Å20.0361 Å20.023 Å2-0.1136 Å20.0078 Å2--0.0844 Å2
L1.0497 °2-0.6908 °20.0249 °2-0.8802 °20.0468 °2--0.9886 °2
S-0.0067 Å °0.0859 Å °-0.0287 Å °0.0463 Å °-0.0639 Å °0.0317 Å °0.038 Å °-0.0026 Å °0.0679 Å °
Refinement TLS groupSelection details: all

+
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