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- PDB-9k7h: Crystal structure of dehydrogenase/isomerase FabX from Helicobact... -

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Basic information

Entry
Database: PDB / ID: 9k7h
TitleCrystal structure of dehydrogenase/isomerase FabX from Helicobacter pylori in complex with inhibitor 1872
Components2-nitropropane dioxygenase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid dehydrogenase/isomerase
Function / homology
Function and homology information


nitronate monooxygenase activity / dioxygenase activity / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / 2-nitropropane dioxygenase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Adv Sci / Year: 2025
Title: Antagonist Targeting the Species-Specific Fatty Acid Dehydrogenase/Isomerase FabX for Anti-H. pylori Infection.
Authors: Zhang, L. / Ruan, X. / Hang, X. / Heng, D. / Cai, C. / Zeng, L. / Zhang, G. / Zhou, L. / Bi, H. / Zhang, L.
History
DepositionOct 23, 2024Deposition site: PDBJ / Processing site: PDBC
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: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9864
Polymers40,7401
Non-polymers1,2463
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-21 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.175, 48.505, 75.897
Angle α, β, γ (deg.)90.00, 93.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-nitropropane dioxygenase / Nitronate monooxygenase


Mass: 40740.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: B0X24_07955, C2840_03950, C2842_03950, DD776_04195, ECB91_05230, ECC12_03705, SE88_03940
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B2E3F3
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-A1EEQ / 3-[[2-[(2,4-dichlorophenyl)amino]pyridin-3-yl]sulfonylamino]benzoic acid


Mass: 438.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13Cl2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, pH 7.0, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.6→41.22 Å / Num. obs: 41739 / % possible obs: 92.6 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Rrim(I) all: 0.068 / Χ2: 0.95 / Net I/σ(I): 16.4 / Num. measured all: 246075
Reflection shellResolution: 1.6→1.69 Å / % possible obs: 72.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.417 / Num. measured all: 20033 / Num. unique obs: 4733 / CC1/2: 0.865 / Rpim(I) all: 0.226 / Rrim(I) all: 0.479 / Χ2: 0.58 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.32 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 2168 5.25 %
Rwork0.2186 --
obs0.2202 41270 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 67 217 3008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082871
X-RAY DIFFRACTIONf_angle_d1.0823896
X-RAY DIFFRACTIONf_dihedral_angle_d10.462422
X-RAY DIFFRACTIONf_chiral_restr0.072428
X-RAY DIFFRACTIONf_plane_restr0.009492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3372980.27281858X-RAY DIFFRACTION66
1.64-1.680.27081230.22942173X-RAY DIFFRACTION77
1.68-1.730.24531490.21732558X-RAY DIFFRACTION91
1.73-1.780.22811460.20782830X-RAY DIFFRACTION100
1.78-1.840.24981660.21462824X-RAY DIFFRACTION100
1.84-1.90.28941660.2312794X-RAY DIFFRACTION99
1.9-1.980.3572740.25621572X-RAY DIFFRACTION55
1.98-2.070.27171520.22812842X-RAY DIFFRACTION100
2.07-2.180.28411610.22012835X-RAY DIFFRACTION100
2.18-2.310.36611350.34742519X-RAY DIFFRACTION88
2.31-2.490.27941760.22642817X-RAY DIFFRACTION100
2.49-2.740.25421680.22932812X-RAY DIFFRACTION100
2.74-3.140.22311170.22242917X-RAY DIFFRACTION100
3.14-3.950.23521460.1952858X-RAY DIFFRACTION99
3.95-30.320.18911910.17092893X-RAY DIFFRACTION99

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