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- PDB-7e1q: Crystal structure of dehydrogenase/isomerase FabX from Helicobact... -

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Basic information

Entry
Database: PDB / ID: 7e1q
TitleCrystal structure of dehydrogenase/isomerase FabX from Helicobacter pylori
Components2-nitropropane dioxygenase
KeywordsFLAVOPROTEIN / Unsaturated fatty acid / FMN / 4Fe-4S cluster
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: 1.7 Å
AuthorsZhou, J.S. / Zhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Nat Commun / Year: 2021
Title: Helicobacter pylori FabX contains a [4Fe-4S] cluster essential for unsaturated fatty acid synthesis.
Authors: Zhou, J. / Zhang, L. / Zeng, L. / Yu, L. / Duan, Y. / Shen, S. / Hu, J. / Zhang, P. / Song, W. / Ruan, X. / Jiang, J. / Zhang, Y. / Zhou, L. / Jia, J. / Hang, X. / Tian, C. / Lin, H. / Chen, ...Authors: Zhou, J. / Zhang, L. / Zeng, L. / Yu, L. / Duan, Y. / Shen, S. / Hu, J. / Zhang, P. / Song, W. / Ruan, X. / Jiang, J. / Zhang, Y. / Zhou, L. / Jia, J. / Hang, X. / Tian, C. / Lin, H. / Chen, H.Z. / Cronan, J.E. / Bi, H. / Zhang, L.
History
DepositionFeb 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7154
Polymers40,8711
Non-polymers8433
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-21 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.829, 65.953, 68.891
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-nitropropane dioxygenase / FabX / Nitronate monooxygenase


Mass: 40871.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: AM497_02530, B0X24_07955, B0X43_08370, BB415_05730, BB461_06560, BV499_05860, BZK23_04525, C2840_03950, C2844_03945, C2S07_02490, DB320_04065, DD749_04060, DD750_03440, DD754_03975, DD776_ ...Gene: AM497_02530, B0X24_07955, B0X43_08370, BB415_05730, BB461_06560, BV499_05860, BZK23_04525, C2840_03950, C2844_03945, C2S07_02490, DB320_04065, DD749_04060, DD750_03440, DD754_03975, DD776_04195, DD780_03830, EC524_01920, EC526_01900, EC558_05290, ECB91_05230, ECC12_03705, ECC36_03060, EGW00_07215, HPY1846_07480
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B2E3F3
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.02 %
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: 0.9785 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.7→68.891 Å / Num. obs: 41292 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.986 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 4148 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IQL

4iql


Resolution: 1.7→42.57 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1733 2069 5.01 %
Rwork0.1441 39223 -
obs0.1455 41292 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.26 Å2 / Biso mean: 17.2241 Å2 / Biso min: 6.32 Å2
Refinement stepCycle: final / Resolution: 1.7→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 40 494 3347
Biso mean--11.08 28.06 -
Num. residues----366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.740.2061190.187229587
1.74-1.780.19781320.1729251694
1.78-1.830.2191400.1676253097
1.83-1.890.18731430.15192626100
1.89-1.950.18611400.14462646100
1.95-2.020.15961440.14442636100
2.02-2.10.17081360.14412609100
2.1-2.190.16661330.14312683100
2.19-2.310.1821410.14422661100
2.31-2.450.19251420.14392644100
2.45-2.640.19391320.14422657100
2.64-2.910.17411400.14622666100
2.91-3.330.16811360.1472660100
3.33-4.190.13811330.12372671100
4.2-42.570.17141580.14162723100

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