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- PDB-7e1r: Crystal structure of Dehydrogenase/isomerase FabX from Helicobact... -

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Basic information

Entry
Database: PDB / ID: 7e1r
TitleCrystal structure of Dehydrogenase/isomerase FabX from Helicobacter pylori in complex with holo-ACP
Components
  • 2-nitropropane dioxygenase
  • Acyl carrier protein,Acyl carrier protein
KeywordsFLAVOPROTEIN / Unsaturated fatty acid biosynthesis / FMN / 4Fe-4S cluster
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / nitronate monooxygenase activity / dioxygenase activity / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding ...Kdo2-lipid A biosynthetic process / nitronate monooxygenase activity / dioxygenase activity / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site ...Nitronate monooxygenase / Nitronate monooxygenase / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-PN7 / IRON/SULFUR CLUSTER / Acyl carrier protein / 2-nitropropane dioxygenase / Acyl carrier protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-nitropropane dioxygenase
B: Acyl carrier protein,Acyl carrier protein
C: 2-nitropropane dioxygenase
D: Acyl carrier protein,Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,80210
Polymers100,4704
Non-polymers2,3336
Water79344
1
A: 2-nitropropane dioxygenase
B: Acyl carrier protein,Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4015
Polymers50,2352
Non-polymers1,1663
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2-nitropropane dioxygenase
D: Acyl carrier protein,Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4015
Polymers50,2352
Non-polymers1,1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.793, 104.443, 99.576
Angle α, β, γ (deg.)90.000, 99.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 40871.305 Da / Num. of mol.: 2
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: Protein Acyl carrier protein,Acyl carrier protein / ACP / ACP


Mass: 9363.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of 2 ACP (residues 1-35 and 36-78)
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: acpP, AOD76_0203840, ECC46_04805, acpP, ACM27_07645, AEY52_04040, B0X51_03260, B0X63_05470, BB389_02970, BB399_05955, BB436_06630, BFR58_08310, BGL65_04100, BGL68_01550, C2R80_01075, C2S26_ ...Gene: acpP, AOD76_0203840, ECC46_04805, acpP, ACM27_07645, AEY52_04040, B0X51_03260, B0X63_05470, BB389_02970, BB399_05955, BB436_06630, BFR58_08310, BGL65_04100, BGL68_01550, C2R80_01075, C2S26_06440, D2C76_07900, DB320_02975, DD746_02765, DD771_02980, EC538_03680, EC543_05790, EC570_04560, EC596_03965, EC600_01035, ECC09_04825, ECC20_05115, ECC36_06460, HPF20_0453, HPF211_0816, HPF63_0811, HPF94_0692, HPK25_01094, HPMKF3_0586, HPMKM1_0566, HPMKM6_0558, HPY1198_07760, NCTC12823_00687
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T6M3S8, UniProt: A0A0B2DUK3

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Non-polymers , 4 types, 50 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-PN7 / N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 20% w/v PEG 8000

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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 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.795→99.576 Å / Num. obs: 21529 / % possible obs: 97.2 % / Redundancy: 6.6 % / CC1/2: 0.987 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2310 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IQL

4iql


Resolution: 2.795→48.736 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1104 5.13 %
Rwork0.2063 20425 -
obs0.2082 21529 82.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.65 Å2 / Biso mean: 49.8445 Å2 / Biso min: 9.15 Å2
Refinement stepCycle: final / Resolution: 2.795→48.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6773 0 78 44 6895
Biso mean--28.75 34.83 -
Num. residues----875
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.795-2.9220.3978830.282145948
2.922-3.0760.31151090.2881192163
3.076-3.26870.29021120.2494231275
3.2687-3.5210.281640.2377266587
3.521-3.87520.24331650.2122298497
3.8752-4.43560.24181490.1901293196
4.4356-5.58710.20381660.17853086100
5.5871-48.7360.20261560.1823306797

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