[English] 日本語
Yorodumi
- PDB-6sl8: Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sl8
TitleDiaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its substrate L-2,4-diaminobutyric acid (DAB)
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
2,4-DIAMINOBUTYRIC ACID / L-2,4-diaminobutyric acid acetyltransferase
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 19, 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 2.0Jun 30, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_poly ...entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.1Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2257
Polymers20,8271
Non-polymers3976
Water2,630146
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)42,44914
Polymers41,6552
Non-polymers79512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4130 Å2
ΔGint-79 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.979, 57.979, 134.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 20827.402 Da / Num. of mol.: 1
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-DAB / 2,4-DIAMINOBUTYRIC ACID


Type: L-peptide linking / Mass: 118.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium sulphate, 20 % (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.5, 20 mM L-2,4-diaminobutyrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.51→53.24 Å / Num. obs: 36817 / % possible obs: 99.9 % / Redundancy: 8.8 % / Rsym value: 0.053 / Net I/σ(I): 16.64
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 1.32 / Num. unique obs: 5756 / Rsym value: 1.453 / % possible all: 99.9

-
Processing

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

6sll


Resolution: 1.53→53.24 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.623 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.07
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1736 4.9 %RANDOM
Rwork0.1775 ---
obs0.1792 33578 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.93 Å2 / Biso mean: 31.658 Å2 / Biso min: 19.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.53→53.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 25 146 1438
Biso mean--42.11 40.1 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191363
X-RAY DIFFRACTIONr_bond_other_d0.0030.021280
X-RAY DIFFRACTIONr_angle_refined_deg2.3451.9571850
X-RAY DIFFRACTIONr_angle_other_deg1.16332941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7222.42466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69415221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1371514
X-RAY DIFFRACTIONr_chiral_restr0.1450.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211551
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02339
LS refinement shellResolution: 1.531→1.571 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 120 -
Rwork0.31 2435 -
all-2555 -
obs--99.34 %

+
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