[English] 日本語
Yorodumi
- PDB-6sjy: Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sjy
TitleDiaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its product ADABA
ComponentsL-2,4-diaminobutyric acid acetyltransferase
KeywordsTRANSFERASE / L-2 / 4-diaminobutyrate acetyltransferase / acetyl coenzyme A / acetylation / stress response / chemical chaperone
Function / homology
Function and homology information


diaminobutyrate acetyltransferase / diaminobutyrate acetyltransferase activity / ectoine biosynthetic process
Similarity search - Function
L-2,4-diaminobutyric acid acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2~{S})-4-acetamido-2-azanyl-butanoic acid / L-2,4-diaminobutyric acid acetyltransferase
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRichter, A.A. / Kobus, S. / Czech, L. / Hoeppner, A. / Bremer, E. / Smits, S.H.J.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine.
Authors: Richter, A.A. / Kobus, S. / Czech, L. / Hoeppner, A. / Zarzycki, J. / Erb, T.J. / Lauterbach, L. / Dickschat, J.S. / Bremer, E. / Smits, S.H.J.
History
DepositionAug 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 30, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Jan 24, 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-2,4-diaminobutyric acid acetyltransferase
C: L-2,4-diaminobutyric acid acetyltransferase
B: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,69410
Polymers60,8163
Non-polymers8797
Water3,963220
1
A: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules

A: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0486
Polymers40,5442
Non-polymers5054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area15020 Å2
MethodPISA
2
B: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules

C: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1707
Polymers40,5442
Non-polymers6275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
Buried area3700 Å2
ΔGint-21 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.214, 174.214, 60.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein L-2,4-diaminobutyric acid acetyltransferase / DABA acetyltransferase


Mass: 20271.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. (strain Y412MC10) (bacteria)
Strain: Y412MC10 / Gene: ectA, GYMC10_5665 / Production host: Escherichia coli (E. coli)
References: UniProt: D3EKC1, diaminobutyrate acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-9YT / (2~{S})-4-acetamido-2-azanyl-butanoic acid


Mass: 160.171 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulphate, 0.085 M MES pH 6.5, 25.5 % (w/v) PEG 5000 MME, 15 % (v/v) glycerol, 20 mM N-gamma-acetyl-2,4-diaminobutyrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→123.2 Å / Num. obs: 61331 / % possible obs: 99.4 % / Redundancy: 11.67 % / Rsym value: 0.088 / Net I/σ(I): 16.75
Reflection shellResolution: 2.02→2.15 Å / Redundancy: 11.07 % / Mean I/σ(I) obs: 2.46 / Num. unique obs: 9451 / Rsym value: 1.08 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SLK

6slk


Resolution: 2.2→123.19 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.972 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1568 3.3 %RANDOM
Rwork0.1674 ---
obs0.1687 46615 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.41 Å2 / Biso mean: 43.688 Å2 / Biso min: 25.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→123.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3931 0 59 220 4210
Biso mean--62.49 48.55 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194112
X-RAY DIFFRACTIONr_bond_other_d0.0030.023764
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.9525579
X-RAY DIFFRACTIONr_angle_other_deg1.14538651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13823.093194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95315630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0771534
X-RAY DIFFRACTIONr_chiral_restr0.1460.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02985
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 114 -
Rwork0.225 3399 -
all-3513 -
obs--99.91 %

+
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