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

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Basic information

Entry
Database: PDB / ID: 9jsy
TitleCrystal structure of dehydrogenase/isomerase FabX from Helicobacter pylori in complex with inhibitor 1991
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: 2 Å
Authorszhang, L. / Zhang, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22477077 China
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 1, 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)41,0735
Polymers39,7881
Non-polymers1,2854
Water4,576254
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 area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.983, 65.538, 53.284
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-nitropropane dioxygenase / Nitronate monooxygenase


Mass: 39788.039 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

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Non-polymers , 5 types, 258 molecules

#2: Chemical ChemComp-A1ECY / methyl 3-[[2-[(2,4-dichlorophenyl)amino]pyridin-3-yl]sulfonylamino]benzoate


Mass: 452.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15Cl2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS-HCL, 25% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24002 / % possible obs: 98.3 % / Redundancy: 6 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.047 / Rrim(I) all: 0.118 / Χ2: 0.933 / Net I/σ(I): 6.7 / Num. measured all: 145111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.074.70.3921420.8860.9690.1910.4361.02488.7
2.07-2.155.20.32923300.9260.9810.1540.3651.01295.4
2.15-2.255.40.27823760.9460.9860.1290.3071.04398.8
2.25-2.3760.24424210.960.990.1080.2671.00899.9
2.37-2.526.50.19124660.9790.9950.0810.2080.958100
2.52-2.716.30.15324260.9830.9960.0660.1660.909100
2.71-2.996.40.11924280.9890.9970.050.1290.827100
2.99-3.426.70.08924380.9920.9980.0370.0960.744100
3.42-4.316.60.06824680.9930.9980.0290.0740.66100
4.31-506.40.08125070.9880.9970.0350.0891.245100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.36 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1947 1082 4.72 %
Rwork0.1615 --
obs0.1631 22901 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 30 254 2996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092802
X-RAY DIFFRACTIONf_angle_d1.123797
X-RAY DIFFRACTIONf_dihedral_angle_d16.1181058
X-RAY DIFFRACTIONf_chiral_restr0.072420
X-RAY DIFFRACTIONf_plane_restr0.01479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.2493900.18611972X-RAY DIFFRACTION68
2.09-2.20.22331120.17482460X-RAY DIFFRACTION84
2.2-2.340.23891250.17242781X-RAY DIFFRACTION95
2.34-2.520.20981340.17022920X-RAY DIFFRACTION99
2.52-2.770.20221250.17152914X-RAY DIFFRACTION99
2.77-3.170.19841470.1752904X-RAY DIFFRACTION100
3.17-3.990.20731650.15312920X-RAY DIFFRACTION100
3.99-26.360.16171840.14582948X-RAY DIFFRACTION100

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