[English] 日本語
Yorodumi
- PDB-5onm: Crystal Structure of Ectoine Synthase from P. lautus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5onm
TitleCrystal Structure of Ectoine Synthase from P. lautus
ComponentsL-ectoine synthase
KeywordsMETAL BINDING PROTEIN / Ectoine / synthase / osmolyte
Function / homology
Function and homology information


ectoine synthase / ectoine synthase activity / ectoine biosynthetic process
Similarity search - Function
Ectoine synthase / Ectoine synthase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / L-ectoine synthase
Similarity search - Component
Biological speciesPaenibacillus lautus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBremer, E.
CitationJournal: Sci Rep / Year: 2019
Title: Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis.
Authors: Czech, L. / Hoppner, A. / Kobus, S. / Seubert, A. / Riclea, R. / Dickschat, J.S. / Heider, J. / Smits, S.H.J. / Bremer, E.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-ectoine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7403
Polymers15,5881
Non-polymers1522
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, dimeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-32 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.130, 71.130, 68.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein L-ectoine synthase / N-acetyldiaminobutyrate dehydratase


Mass: 15587.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus lautus (bacteria) / Gene: ectC, BK123_26285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R1AV52, ectoine synthase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.2
Details: 0.2 M ammonium sulfate, 0.1 M phosphate citrate pH 4.2, 20% (v/v) PEG 300, 10% (v/v) glycerol.
PH range: 4.0-5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.52→35.565 Å / Num. obs: 31125 / % possible obs: 99.3 % / Redundancy: 18.8 % / Net I/σ(I): 19.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BXX

5bxx


Resolution: 1.52→35.565 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2028 2010 6.46 %
Rwork0.1758 --
obs0.1776 31108 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.52→35.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 6 133 1231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111150
X-RAY DIFFRACTIONf_angle_d1.4051568
X-RAY DIFFRACTIONf_dihedral_angle_d13.857417
X-RAY DIFFRACTIONf_chiral_restr0.056171
X-RAY DIFFRACTIONf_plane_restr0.006200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.5580.28241390.27151985X-RAY DIFFRACTION97
1.558-1.60020.25861420.24162079X-RAY DIFFRACTION100
1.6002-1.64720.28841460.23432070X-RAY DIFFRACTION100
1.6472-1.70040.29171420.2432078X-RAY DIFFRACTION100
1.7004-1.76120.32961290.30681921X-RAY DIFFRACTION93
1.7612-1.83170.24581460.20152075X-RAY DIFFRACTION100
1.8317-1.91510.21421400.18192061X-RAY DIFFRACTION100
1.9151-2.0160.19961460.17372088X-RAY DIFFRACTION100
2.016-2.14230.18771460.17322086X-RAY DIFFRACTION100
2.1423-2.30770.2011450.16712102X-RAY DIFFRACTION100
2.3077-2.53990.20771410.15822094X-RAY DIFFRACTION100
2.5399-2.90720.18241460.17442102X-RAY DIFFRACTION100
2.9072-3.66220.21431470.16182135X-RAY DIFFRACTION100
3.6622-35.57470.15691550.14952222X-RAY DIFFRACTION100

+
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