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- PDB-9my6: Structure of the BasE double mutant V336A/S247C, an NRPS adenylat... -

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Basic information

Entry
Database: PDB / ID: 9my6
TitleStructure of the BasE double mutant V336A/S247C, an NRPS adenylation domain in the acinetobactin biosynthetic pathway bound to 4-fluoro 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
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
: / DI(HYDROXYETHYL)ETHER / (2,3-dihydroxybenzoyl)adenylate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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)126,77815
Polymers125,8712
Non-polymers90713
Water3,855214
1
B: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3186
Polymers62,9351
Non-polymers3825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4609
Polymers62,9351
Non-polymers5258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.424, 141.246, 148.464
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

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Protein , 1 types, 2 molecules BA

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


Mass: 62935.480 Da / Num. of mol.: 2 / Mutation: P45L, S247C, 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

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Non-polymers , 5 types, 227 molecules

#2: Chemical ChemComp-OOI / 4-fluorosalicyclic acid / 4-fluoranyl-2-oxidanyl-benzoic acid / 4-Fluoro-2-hydroxybenzoic Acid


Mass: 156.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5FO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.86 %
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-fluorosalicylic 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: Jul 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.07→102.33 Å / Num. obs: 80620 / % possible obs: 95.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 39.79 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.04 / Net I/σ(I): 10.8
Reflection shellResolution: 2.07→2.19 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.068 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12154 / CC1/2: 0.853 / Rpim(I) all: 0.534 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→63.78 Å / SU ML: 0.2402 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 1996 2.49 %
Rwork0.1912 78154 -
obs0.1919 80150 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.37 Å2
Refinement stepCycle: LAST / Resolution: 2.07→63.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6754 0 48 214 7016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01056975
X-RAY DIFFRACTIONf_angle_d1.06239498
X-RAY DIFFRACTIONf_chiral_restr0.06131063
X-RAY DIFFRACTIONf_plane_restr0.01041245
X-RAY DIFFRACTIONf_dihedral_angle_d8.3833959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.120.34771470.30985725X-RAY DIFFRACTION99.07
2.12-2.180.30771480.28325764X-RAY DIFFRACTION99.09
2.18-2.250.31641320.27985038X-RAY DIFFRACTION86.89
2.25-2.320.31981440.26145691X-RAY DIFFRACTION98.18
2.32-2.40.26941380.23545712X-RAY DIFFRACTION98.63
2.4-2.50.21071530.21245645X-RAY DIFFRACTION96.88
2.5-2.610.29081440.21465723X-RAY DIFFRACTION98.23
2.61-2.750.24741130.21324833X-RAY DIFFRACTION82.63
2.75-2.920.22881550.21575776X-RAY DIFFRACTION99.23
2.92-3.150.24421470.20855828X-RAY DIFFRACTION99.43
3.15-3.460.23151420.1995212X-RAY DIFFRACTION88.2
3.46-3.970.20911240.17885160X-RAY DIFFRACTION87.6
3.97-50.1791520.14795976X-RAY DIFFRACTION99.87
5-63.780.1691570.16386071X-RAY DIFFRACTION97.89
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)
11.264480904730.67032912720.1730030258732.085134214330.05556473151752.64361400950.02503506860260.0265058557933-0.0829596411510.1559699598580.0244839373192-0.1526366421320.01630152463150.003964730588-0.04375894282210.2531885300190.0508867725708-0.004314310711330.311080420963-0.01249457297910.256901916954-23.7459108733-12.362655938519.2708118225
21.31247345689-0.093963687061-0.314425329031.88646307146-0.1337118042961.957430411690.0230763682014-0.127325467315-0.0011755951294-0.137323515186-0.0625273111073-0.182605699687-0.05940882461620.425472704850.03749289763760.314668047826-0.01293142210460.02759379135830.4517836822120.02452148411180.227174005436-5.23634347691-9.0166477989-12.3280066631
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 3 - 438 / Label seq-ID: 1 - 436

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'B' and resid 3 through 438)BA
22(chain 'A' and resid 3 through 438)AD

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