[English] 日本語
Yorodumi
- PDB-5by5: High resolution structure of the ectoine synthase from the cold-a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5by5
TitleHigh resolution structure of the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis
ComponentsL-ectoine synthase
KeywordsLYASE / Compatible solute - Osmostress protectant - Chemical chaperone - Enzyme - Ectoine synthesis - Cupin - X-ray analysis
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
S-1,2-PROPANEDIOL / L-ectoine synthase
Similarity search - Component
Biological speciesSphingopyxis alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsWidderich, N. / Kobus, S. / Hoeppner, A. / Bremer, E. / Smits, S.H.J.
CitationJournal: Plos One / Year: 2016
Title: Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily.
Authors: Widderich, N. / Kobus, S. / Hoppner, A. / Riclea, R. / Seubert, A. / Dickschat, J.S. / Heider, J. / Smits, S.H. / Bremer, E.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2May 8, 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: L-ectoine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8608
Polymers16,3271
Non-polymers5337
Water2,000111
1
A: L-ectoine synthase
hetero molecules

A: L-ectoine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72016
Polymers32,6552
Non-polymers1,06514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)72.710, 72.710, 52.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 16327.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (bacteria)
Gene: ectC, Sala_2951 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GNW6, ectoine synthase
#2: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 285 K / Method: vapor diffusion
Details: 0.05 M calcium acetate, 0.1 M sodium acetate pH 6, 40% (v/v) 1,2-propanediol
PH range: 4.5-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.2→19.4 Å / Num. obs: 49094 / % possible obs: 97.82 % / Redundancy: 7.6 % / Net I/σ(I): 21.94

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.2→19.4 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.752 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14929 616 1.3 %RANDOM
Rwork0.12423 ---
obs0.12456 48490 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.2→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 35 111 1047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191004
X-RAY DIFFRACTIONr_bond_other_d0.0020.021018
X-RAY DIFFRACTIONr_angle_refined_deg2.1871.9711353
X-RAY DIFFRACTIONr_angle_other_deg0.9543.0012291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07722.55347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46815172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1961511
X-RAY DIFFRACTIONr_chiral_restr0.1350.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4651.112488
X-RAY DIFFRACTIONr_mcbond_other2.4121.101487
X-RAY DIFFRACTIONr_mcangle_it3.4881.673617
X-RAY DIFFRACTIONr_mcangle_other3.4971.683618
X-RAY DIFFRACTIONr_scbond_it6.0721.899516
X-RAY DIFFRACTIONr_scbond_other6.0711.908517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7922.588737
X-RAY DIFFRACTIONr_long_range_B_refined6.74312.1911121
X-RAY DIFFRACTIONr_long_range_B_other6.54311.7871080
X-RAY DIFFRACTIONr_rigid_bond_restr5.02132021
X-RAY DIFFRACTIONr_sphericity_free43.649527
X-RAY DIFFRACTIONr_sphericity_bonded16.32752091
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 32 -
Rwork0.177 3442 -
obs--94.4 %

+
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