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- PDB-9my5: Structure of the BasE mutant V336A, an NRPS adenylation domain in... -

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Basic information

Entry
Database: PDB / ID: 9my5
TitleStructure of the BasE mutant V336A, an NRPS adenylation domain in the acinetobactin biosynthetic pathway bound to 4-methyl salicylic Acid
Components(2,3-dihydroxybenzoyl)adenylate synthase
KeywordsLIGASE / NRPS / Adenylation Domain / Nonribosomal peptide siderophore / acinetobactin / synthetase
Function / homology
Function and homology information


(2,3-dihydroxybenzoyl)adenylate synthase / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process / nucleotidyltransferase activity / ATP binding
Similarity search - Function
2,3-dihydroxybenzoate-AMP ligase / : / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
: / (2,3-dihydroxybenzoyl)adenylate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsAhmed, S.F. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136235 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: The structural basis of substrate selectivity of the acinetobactin biosynthetic adenylation domain, BasE.
Authors: Ahmed, S.F. / Gulick, A.M.
History
DepositionJan 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: (2,3-dihydroxybenzoyl)adenylate synthase
A: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,48612
Polymers125,8392
Non-polymers64710
Water5,188288
1
B: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2947
Polymers62,9191
Non-polymers3756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1925
Polymers62,9191
Non-polymers2724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.759, 143.682, 148.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein (2,3-dihydroxybenzoyl)adenylate synthase / 2 / 3-dihydroxybenzoate-AMP ligase


Mass: 62919.418 Da / Num. of mol.: 2 / Mutation: P45L, V336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB900 / Gene: entE, basE, ABR2091_2618, GSE42_14350, H0529_00955
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A505MWF2, (2,3-dihydroxybenzoyl)adenylate synthase
#2: Chemical ChemComp-A1BUB / 2-hydroxy-4-methylbenzoic acid / 4-methyl salicylic acid


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN
Sequence detailsThis entry uses a Uniprot reference that is for a different strain of A. Baumannii. These sequence ...This entry uses a Uniprot reference that is for a different strain of A. Baumannii. These sequence discrepancies listed as "conflicts" are due to this strain difference. The wild-type sequence for the protein from this strain of A. Baumannii is found in Genbank entry WP_000744385.1.

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12% PEG 4000, 0.1 M Calcium chloride, 0.05 M TRIS HCl pH 8.5, 3mM 4-methylsalicylic acid

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.39→39.59 Å / Num. obs: 56567 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 49.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.041 / Net I/σ(I): 14
Reflection shellResolution: 2.39→2.46 Å / Rmerge(I) obs: 1.462 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4575 / CC1/2: 0.728 / Rpim(I) all: 0.629

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→39.59 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 2001 3.55 %
Rwork0.1861 54422 -
obs0.1874 56423 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.06 Å2
Refinement stepCycle: LAST / Resolution: 2.39→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6715 0 33 288 7036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826905
X-RAY DIFFRACTIONf_angle_d0.90879410
X-RAY DIFFRACTIONf_chiral_restr0.05341062
X-RAY DIFFRACTIONf_plane_restr0.00821233
X-RAY DIFFRACTIONf_dihedral_angle_d7.2901951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.35041480.30553820X-RAY DIFFRACTION99.77
2.45-2.520.27191340.27273858X-RAY DIFFRACTION99.75
2.52-2.590.3011410.25633840X-RAY DIFFRACTION99.9
2.59-2.670.27771440.24493824X-RAY DIFFRACTION99.6
2.67-2.770.29791350.24133865X-RAY DIFFRACTION99.8
2.77-2.880.26041460.23413804X-RAY DIFFRACTION98.73
2.88-3.010.25111410.21093866X-RAY DIFFRACTION99.5
3.01-3.170.25881400.20363851X-RAY DIFFRACTION99.85
3.17-3.370.24271450.20753879X-RAY DIFFRACTION99.88
3.37-3.630.2041400.19123917X-RAY DIFFRACTION99.9
3.63-3.990.21551410.16333892X-RAY DIFFRACTION99.9
3.99-4.570.17761450.1493891X-RAY DIFFRACTION99.12
4.57-5.750.2171460.15423997X-RAY DIFFRACTION100
5.76-39.590.19841550.16564118X-RAY DIFFRACTION99.14
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.241713023290.4322518989280.1390747471891.77656835378-0.0528750187252.326030623280.03534047558520.0363196893484-0.08504374773730.05303927624940.0051746579826-0.1629496039440.04605533380880.0899758638719-0.03876212872090.3125322422280.03305093192730.00733797081480.343969847484-0.02102457566720.370378629861-23.928165643-12.780405226219.3233183797
21.50258426677-0.213431948769-0.2723482344492.16636735904-0.08391842544062.6223604104-0.0471923007452-0.172114382778-0.0677223301977-0.011791535511-0.0332442916606-0.08770061718910.1351675332590.2511733994890.07144708009670.280864935334-0.002123264788740.04003972490210.3571709195180.02740365038860.287739117727-5.19634026056-9.57820191029-12.5455920272
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 3 through 439)BA - B3 - 5011
22(chain 'A' and resid 3 through 439)AD3 - 4391 - 437

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