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

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Basic information

Entry
Database: PDB / ID: 9bhy
TitleStructure of FbsH, an NRPS adenylation domain in the fimsbactin biosynthetic pathway bound to 2,3-dihydroxybenzoic acid.
Components2,3-dihydroxybenzoate-AMP ligase
KeywordsLIGASE/SUBSTRATE / NRPS Adenylation Domain Nonribosomal peptide siderophore Inhibitor / LIGASE / LIGASE-SUBSTRATE 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
2,3-DIHYDROXY-BENZOIC ACID / 2,3-dihydroxybenzoate-AMP ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)129,0606
Polymers128,6282
Non-polymers4324
Water3,297183
1
A: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5303
Polymers64,3141
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5303
Polymers64,3141
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.410, 74.478, 75.493
Angle α, β, γ (deg.)85.040, 69.890, 70.290
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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
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-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4 / 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.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN
Sequence detailsThe protein contains an uncleaved, N-terminal His-tag thrombin cleavage site, and T7 tag.

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 12% PEG 3350, 0.5 mM DHB, 0.5 mM AMP

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Data collection

DiffractionMean temperature: 93.15 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: 2.3→35.62 Å / Num. obs: 47445 / % possible obs: 98.25 % / Redundancy: 3.5 % / Biso Wilson estimate: 42 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.08125 / Rrim(I) all: 0.1523 / Net I/σ(I): 10.32
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.9187 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 4701 / CC1/2: 0.44 / CC star: 0.782 / Rpim(I) all: 0.5656 / Rrim(I) all: 1 / % possible all: 97.14

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.62 Å / SU ML: 0.2852 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.7303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 2239 4.72 %
Rwork0.1926 88435 -
obs0.1943 47424 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7747 0 30 183 7960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427926
X-RAY DIFFRACTIONf_angle_d0.630910792
X-RAY DIFFRACTIONf_chiral_restr0.04721261
X-RAY DIFFRACTIONf_plane_restr0.00491398
X-RAY DIFFRACTIONf_dihedral_angle_d8.78021109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.30931820.26532925X-RAY DIFFRACTION94.04
2.33-2.350.29961390.25562890X-RAY DIFFRACTION93.89
2.35-2.380.2921440.25012816X-RAY DIFFRACTION94.75
2.38-2.410.30881600.26312997X-RAY DIFFRACTION95.09
2.41-2.440.31251620.24442834X-RAY DIFFRACTION94.81
2.44-2.480.29422260.24792872X-RAY DIFFRACTION95.38
2.48-2.510.29131790.24582841X-RAY DIFFRACTION95.27
2.51-2.550.28941870.23792935X-RAY DIFFRACTION96.06
2.55-2.590.29241780.23482849X-RAY DIFFRACTION95.13
2.59-2.630.30761510.22982909X-RAY DIFFRACTION96.29
2.63-2.680.25721470.23022931X-RAY DIFFRACTION95.29
2.68-2.730.32121630.23192924X-RAY DIFFRACTION95.75
2.73-2.780.29261370.21792878X-RAY DIFFRACTION95.84
2.78-2.840.27391650.21463036X-RAY DIFFRACTION95.72
2.84-2.90.25811240.20422921X-RAY DIFFRACTION96.67
2.9-2.960.23461510.20753034X-RAY DIFFRACTION96.11
2.96-3.040.2567850.20572909X-RAY DIFFRACTION96.64
3.04-3.120.22751230.19673061X-RAY DIFFRACTION96.6
3.12-3.210.24341210.20052959X-RAY DIFFRACTION97.1
3.21-3.320.2764510.19043088X-RAY DIFFRACTION97.12
3.32-3.430.21041390.19152948X-RAY DIFFRACTION97.57
3.44-3.570.21391540.17622986X-RAY DIFFRACTION97.21
3.57-3.730.24372360.17352936X-RAY DIFFRACTION97.06
3.73-3.930.20781530.1562929X-RAY DIFFRACTION97.35
3.93-4.180.18781040.15633012X-RAY DIFFRACTION97.13
4.18-4.50.1681140.15173009X-RAY DIFFRACTION96.81
4.5-4.950.17751330.15612968X-RAY DIFFRACTION97.15
4.95-5.660.21721290.18733022X-RAY DIFFRACTION96.89
5.67-7.120.2496770.19733005X-RAY DIFFRACTION96.31
7.13-35.620.17251640.16483011X-RAY DIFFRACTION97.99
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)
11.916634038680.3663105622210.2370430913071.75542315694-0.04559328898481.15960119788-0.0256962896144-0.04705533148780.0413610366469-0.1065158729020.0114223511760.0611835547979-0.0312679970069-0.05338384222090.008288613670.146518652994-0.006016740417980.005466682626790.153515500985-0.03303739498290.146453339487-0.1833767581812.892644103517.0672447013
25.96716710072-3.68164103304-0.3167119114685.08207352637-0.3302100744780.4747323587240.5420863451530.224466535288-0.107753542768-0.490256022814-0.1567438320730.02609425205030.2093437509140.0220328168749-0.3586796866290.5306298345820.0776444321169-0.008638260786020.448390212841-0.07573881983650.377227000018-13.535674952245.312780087224.2620395529
32.01748673504-0.203945136583-0.7518689009221.215531857090.2069675021672.881857257180.01807972640280.0268772291181-0.02523326172490.00773912688614-0.04480064900290.0147602082245-0.00857146100295-0.06313878666410.0182331911750.155951518535-0.0205372426329-0.003616564133970.162881072004-0.01152994110890.160313225494-3.8882174944753.330041185355.3986525872
41.991238691970.3226899585840.3214896451940.184308985712-0.1271372832172.654565095780.477275537638-0.396073181701-0.03160640092090.543162036271-0.251708241805-0.0462326592408-0.1429565603710.07634277411-0.2060541238180.704093556921-0.178707687702-0.03258530161520.555548249458-0.1131659930180.556960829338-7.8895093181720.430629494844.3805753935
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 439 )AA1 - 4391 - 437
22chain 'A' and (resid 440 through 524 )AA440 - 524438 - 517
33chain 'B' and (resid 1 through 439 )BD1 - 4391 - 436
44chain 'B' and (resid 440 through 523 )BD440 - 523437 - 513

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