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- PDB-9my7: Structure of the BasE mutant V336G, an NRPS adenylation domain in... -

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Basic information

Entry
Database: PDB / ID: 9my7
TitleStructure of the BasE mutant V336G, an NRPS adenylation domain in the acinetobactin biosynthetic pathway bound to 4-amino 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
2-HYDROXY-4-AMINOBENZOIC ACID / (2,3-dihydroxybenzoyl)adenylate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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)126,66416
Polymers125,8112
Non-polymers85314
Water2,756153
1
B: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3218
Polymers62,9051
Non-polymers4167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: (2,3-dihydroxybenzoyl)adenylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3438
Polymers62,9051
Non-polymers4387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.294, 143.346, 149.199
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 / BasE


Mass: 62905.395 Da / Num. of mol.: 2 / Mutation: P45L, V336G
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-BHA / 2-HYDROXY-4-AMINOBENZOIC ACID


Mass: 153.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
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, 5mM 4-azidosalicylic 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: 2.53→66.17 Å / Num. obs: 47313 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 50.66 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Net I/σ(I): 9.6
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 4 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6822 / CC1/2: 0.522 / Rpim(I) all: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→66.17 Å / SU ML: 0.3527 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 1996 4.24 %
Rwork0.2135 45071 -
obs0.2156 47067 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.4 Å2
Refinement stepCycle: LAST / Resolution: 2.53→66.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 43 153 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00176838
X-RAY DIFFRACTIONf_angle_d0.46069327
X-RAY DIFFRACTIONf_chiral_restr0.03921057
X-RAY DIFFRACTIONf_plane_restr0.00381220
X-RAY DIFFRACTIONf_dihedral_angle_d4.6799950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.590.42781300.36883094X-RAY DIFFRACTION96.7
2.59-2.660.37061490.34183170X-RAY DIFFRACTION99.19
2.66-2.740.32121320.31863198X-RAY DIFFRACTION99.37
2.74-2.830.32851500.2963184X-RAY DIFFRACTION99.58
2.83-2.930.34371440.28563200X-RAY DIFFRACTION99.76
2.93-3.050.32811410.28043190X-RAY DIFFRACTION99.58
3.05-3.190.32741350.25413224X-RAY DIFFRACTION99.73
3.19-3.360.32461490.23533178X-RAY DIFFRACTION98.9
3.36-3.570.25621350.21183207X-RAY DIFFRACTION98.58
3.57-3.840.24331410.19823188X-RAY DIFFRACTION97.85
3.84-4.230.2631450.1773236X-RAY DIFFRACTION99.73
4.23-4.840.18781460.1563265X-RAY DIFFRACTION99.74
4.84-6.10.21551460.1853321X-RAY DIFFRACTION99.88
6.1-66.170.2321530.18653416X-RAY DIFFRACTION98.16
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)
10.8466370125580.6900541496350.0557924870362.05646926787-0.05054100123951.954684746630.08131848688460.132612511606-0.1202462177030.0695835733563-0.00399514533932-0.1805546770510.06475741634410.12687235815-0.0808580982350.3276739963210.0668714997197-0.01241881558980.652418152901-0.01040092138440.405505805899-23.932077464-12.692157989119.3546548218
21.189718556430.172813529811-0.5532084743482.08369098973-0.3946949243911.614719042730.021227699112-0.321795883867-0.0791200515412-0.0254018716178-0.164697208659-0.2623072469830.07089999636630.424621899360.1367079120770.3652229185270.02981336659350.03407085734810.8501263712280.06526565839240.379788785862-5.23866656083-9.26770991099-12.5753812947
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 3 - 437 / Label seq-ID: 1 - 435

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'B' and resid 3 through 437)BA
22(chain 'A' and resid 3 through 437)AD

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