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- PDB-6sk1: Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus ... -

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Basic information

Entry
Database: PDB / ID: 6sk1
TitleDiaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with coenzyme A
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
ACETATE ION / COENZYME A / L-2,4-diaminobutyric acid acetyltransferase
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 2.0Jun 30, 2021Group: Advisory / Database references ...Advisory / Database references / 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_unobs_or_zero_occ_residues / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,6543
Polymers20,8271
Non-polymers8272
Water3,765209
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)43,3086
Polymers41,6552
Non-polymers1,6534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6160 Å2
ΔGint-29 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.282, 68.282, 79.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium chloride, 0.1 M sodium chloride, 12 % (w/v) PEG 4000, 0.1 M tri-sodium citrate pH 5.5, 5 mM coenzyme A

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.13→51.89 Å / Num. obs: 70942 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rsym value: 0.067 / Net I/σ(I): 13.46
Reflection shellResolution: 1.13→1.21 Å / Num. unique obs: 12931 / Rsym value: 1.343 / % possible all: 99.8

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Processing

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

6slk


Resolution: 1.5→51.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.904 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1624 5.3 %RANDOM
Rwork0.1468 ---
obs0.1487 29199 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.23 Å2 / Biso mean: 14.566 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.5→51.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 52 209 1514
Biso mean--14.6 25.34 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0191408
X-RAY DIFFRACTIONr_bond_other_d0.0030.021300
X-RAY DIFFRACTIONr_angle_refined_deg2.5971.9911929
X-RAY DIFFRACTIONr_angle_other_deg1.22232995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92422.18864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7541514
X-RAY DIFFRACTIONr_chiral_restr0.1650.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211586
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02345
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 138 -
Rwork0.143 2090 -
all-2228 -
obs--99.82 %

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