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- PDB-9bhz: Structure of FbsH, an NRPS adenylation domain in the fimsbactin b... -

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Basic information

Entry
Database: PDB / ID: 9bhz
TitleStructure of FbsH, an NRPS adenylation domain in the fimsbactin biosynthetic pathway bound to Salicyl-AMS
Components2,3-dihydroxybenzoate-AMP ligase
KeywordsLIGASE/INHIBITOR / NRPS Adenylation Domain Nonribosomal peptide siderophore Inhibitor / LIGASE / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process
Similarity search - Function
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
5'-O-[(2-hydroxybenzoyl)sulfamoyl]adenosine / 2,3-dihydroxybenzoate-AMP ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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: Acs Chem.Biol. / Year: 2024
Title: Expanding the Substrate Selectivity of the Fimsbactin Biosynthetic Adenylation Domain, FbsH.
Authors: Ahmed, S.F. / Balutowski, A. / Yang, J. / Wencewicz, T.A. / Gulick, A.M.
History
DepositionApr 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3-dihydroxybenzoate-AMP ligase
B: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6856
Polymers128,6282
Non-polymers1,0574
Water3,279182
1
A: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8423
Polymers64,3141
Non-polymers5282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8423
Polymers64,3141
Non-polymers5282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.329, 74.170, 75.557
Angle α, β, γ (deg.)85.05, 69.91, 70.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 2,3-dihydroxybenzoate-AMP ligase


Mass: 64313.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein contains an uncleaved, N-terminal His-tag thrombin cleavage site, and T7 tag.
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 17978 / Gene: AUO97_01775
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5P1UDB1
#2: Chemical ChemComp-KT0 / 5'-O-[(2-hydroxybenzoyl)sulfamoyl]adenosine


Mass: 466.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 0.1 M HEPES pH 7.5, 0.6 mM Salicyl-AMS

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03373 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03373 Å / Relative weight: 1
ReflectionResolution: 2.2→35.58 Å / Num. obs: 52019 / % possible obs: 97.95 % / Redundancy: 3.5 % / Biso Wilson estimate: 42.68 Å2 / CC1/2: 0.968 / CC star: 0.992 / Rmerge(I) obs: 0.1872 / Rpim(I) all: 0.1202 / Rrim(I) all: 0.2234 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 5132 / CC1/2: 0.714 / CC star: 0.913 / Rpim(I) all: 0.7654 / % possible all: 96.05

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→35.58 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1995 3.84 %
Rwork0.1975 --
obs0.1991 51903 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 72 182 7672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087627
X-RAY DIFFRACTIONf_angle_d0.898
X-RAY DIFFRACTIONf_dihedral_angle_d7.0411047
X-RAY DIFFRACTIONf_chiral_restr0.0541201
X-RAY DIFFRACTIONf_plane_restr0.0071334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.32531410.28483497X-RAY DIFFRACTION96
2.28-2.340.35271510.2643534X-RAY DIFFRACTION97
2.34-2.410.28981300.24143521X-RAY DIFFRACTION97
2.41-2.490.26951400.23523521X-RAY DIFFRACTION97
2.49-2.580.31221460.22793574X-RAY DIFFRACTION98
2.58-2.680.28541290.23033560X-RAY DIFFRACTION98
2.68-2.80.25771450.23023553X-RAY DIFFRACTION98
2.8-2.950.24941450.20893573X-RAY DIFFRACTION98
2.95-3.140.27311480.21353590X-RAY DIFFRACTION98
3.14-3.380.27721470.20853569X-RAY DIFFRACTION99
3.38-3.720.23021470.19243589X-RAY DIFFRACTION99
3.72-4.250.19161370.1673596X-RAY DIFFRACTION99
4.25-5.360.19751480.1643601X-RAY DIFFRACTION99
5.36-35.580.21671410.18563630X-RAY DIFFRACTION99
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)
13.23240.1584-2.0285.71171.27849.99190.43210.6935-0.2-0.0724-0.32860.13760.3398-1.233-0.10280.47320.1158-0.0490.7094-0.14430.4971-11.792443.493525.7407
21.70140.5971-0.04042.3354-0.03191.22150.0375-0.04240.0293-0.0392-0.00660.06290.0027-0.0787-0.03060.2061-0.0025-0.02240.2517-0.03650.2234-0.060812.933917.1093
31.9004-0.2144-0.95891.72580.14133.79220.0060.0246-0.0143-0.0229-0.070.0234-0.004-0.05630.05940.2406-0.0389-0.03230.2596-0.02570.25221.6129-14.2996-15.6403
40.5326-0.05050.92530.6288-0.32932.02260.1993-0.3214-0.2539-0.2538-0.03960.02520.468-1.0765-0.15870.9432-0.1931-0.2251.0407-0.22380.8386-4.0185-48.2458-26.085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 440 through 526 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 439 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 439 )
4X-RAY DIFFRACTION4chain 'B' and (resid 451 through 522 )

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