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

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Basic information

Entry
Database: PDB / ID: 6sll
TitleDiaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its substrate L-2,4-diaminobutyric acid (DAB) and 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
COENZYME A / 2,4-DIAMINOBUTYRIC ACID / L-2,4-diaminobutyric acid acetyltransferase
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 20, 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 / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id
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
B: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4507
Polymers41,6552
Non-polymers1,7965
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.048, 151.048, 46.172
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 20827.402 Da / Num. of mol.: 2
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


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION / References: UniProt: D3EKC1*PLUS
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium fluoride, 20 % (w/v) PEG 3350, 5 mM coenzyme A, 20 mM L-2,4-diaminobutyrate

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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: 1.05→75.53 Å / Num. obs: 182408 / % possible obs: 99.2 % / Redundancy: 3.59 % / Rsym value: 0.048 / Net I/σ(I): 10.43
Reflection shellResolution: 1.05→1.11 Å / Mean I/σ(I) obs: 1.59 / Num. unique obs: 27168 / Rsym value: 0.608

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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: 6SK1

6sk1


Resolution: 1.2→75.52 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.999 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1496 6191 5.1 %RANDOM
Rwork0.1218 ---
obs0.1232 116031 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.19 Å2 / Biso mean: 17.319 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.2→75.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 113 543 3248
Biso mean--18.44 31.44 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0192947
X-RAY DIFFRACTIONr_bond_other_d0.0030.022697
X-RAY DIFFRACTIONr_angle_refined_deg3.0241.994043
X-RAY DIFFRACTIONr_angle_other_deg1.56536232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1845377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95322.806139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63715467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6941528
X-RAY DIFFRACTIONr_chiral_restr0.20.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213378
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02724
X-RAY DIFFRACTIONr_rigid_bond_restr7.29435644
X-RAY DIFFRACTIONr_sphericity_free30.515115
X-RAY DIFFRACTIONr_sphericity_bonded11.9955981
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 464 -
Rwork0.256 8358 -
all-8822 -
obs--97.32 %

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