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- PDB-9s5x: Crystal structure of Neisseria gonorrhoeae FabI in complex with N... -

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Basic information

Entry
Database: PDB / ID: 9s5x
TitleCrystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Enoyl-[acyl-carrier-protein] reductase [NADH] Neisseria gonorrhoeae / HYDROLASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 Å
AuthorsRonin, C. / Gerusz, V. / Ciesielski, F.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Other government75A50122C00028 Switzerland
CitationJournal: To Be Published
Title: Discovery of gofabicin: a bactericidal FabI-inhibitor that clears antibiotic-resistant Neisseria gonorrhoeae in vivo
Authors: Ronin, C. / Gerusz, V. / Ciesielski, F.
History
DepositionJul 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2926
Polymers60,1242
Non-polymers2,1684
Water7,422412
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-36 kcal/mol
Surface area20650 Å2
Unit cell
Length a, b, c (Å)91.260, 91.260, 241.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 30062.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC 700825 / Gene: NGO_1666 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5F696, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-A1H1H / (~{E})-~{N}-methyl-~{N}-[(3-methyl-1-benzofuran-2-yl)methyl]-3-[(2~{R},3~{S})-2-methyl-3-oxidanyl-4-oxidanylidene-1,2,3,5-tetrahydropyrido[2,3-b][1,4]diazepin-8-yl]prop-2-enamide / GW409544


Mass: 420.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.41 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 100mM Bicine pH9; 2.4M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.34→75.21 Å / Num. obs: 108279 / % possible obs: 96.9 % / Redundancy: 19.8 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.013 / Rrim(I) all: 0.059 / Net I/σ(I): 26.1
Reflection shellResolution: 1.34→1.445 Å / Redundancy: 19.9 % / Rmerge(I) obs: 2.06 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5415 / CC1/2: 0.655 / Rpim(I) all: 0.472 / Rrim(I) all: 2.114 / % possible all: 77.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.93 Å75.1 Å
Translation4.93 Å75.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHASER2.8.3phasing
PDB_EXTRACT3.28data extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→75.21 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.064 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 5371 5 %RANDOM
Rwork0.1666 ---
obs0.168 102908 81.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.1 Å2 / Biso mean: 20.842 Å2 / Biso min: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.34→75.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 150 412 4398
Biso mean--18.86 32.09 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124091
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163897
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.8085546
X-RAY DIFFRACTIONr_angle_other_deg0.6571.7438946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.4786.29654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96410667
X-RAY DIFFRACTIONr_chiral_restr0.0980.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02931
X-RAY DIFFRACTIONr_mcbond_it1.8962.0032073
X-RAY DIFFRACTIONr_mcbond_other1.8952.0032073
X-RAY DIFFRACTIONr_mcangle_it2.5223.5922593
LS refinement shellResolution: 1.341→1.376 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 29 -
Rwork0.303 438 -
all-467 -
obs--4.84 %

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