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- PDB-7e1s: Crystal structure of dehydrogenase/isomerase FabX from Helicobact... -

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Basic information

Entry
Database: PDB / ID: 7e1s
TitleCrystal structure of dehydrogenase/isomerase FabX from Helicobacter pylori in complex with octanoyl-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 / phosphopantetheine binding / acyl carrier activity / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / 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. ...Nitronate monooxygenase / Nitronate monooxygenase / 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
Similarity search - Domain/homology
Chem-66S / FLAVIN MONONUCLEOTIDE / 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: 2.31 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

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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)103,05510
Polymers100,4704
Non-polymers2,5856
Water3,513195
1
A: 2-nitropropane dioxygenase
B: Acyl carrier protein,Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5275
Polymers50,2352
Non-polymers1,2933
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)51,5275
Polymers50,2352
Non-polymers1,2933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.894, 100.133, 105.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 1-36 and 37-78)
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: acpP, C2S08_00655, 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, ...Gene: acpP, C2S08_00655, 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: A0A2T6RV84, UniProt: A0A0B2DUK3

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Non-polymers , 4 types, 201 molecules

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


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-66S / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate


Mass: 484.544 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H37N2O8PS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES, pH 7.0, 20% PEG 4000

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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: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→105.479 Å / Num. obs: 46632 / % possible obs: 99.8 % / Redundancy: 13.1 % / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.35 Å

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Processing

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

4iql


Resolution: 2.31→72.62 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 2278 4.89 %
Rwork0.233 --
obs0.236 46631 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.64 Å2
Refinement stepCycle: LAST / Resolution: 2.31→72.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 138 195 6684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.3721220.29972751X-RAY DIFFRACTION100
2.36-2.410.30041490.27612719X-RAY DIFFRACTION100
2.41-2.470.37021780.27622689X-RAY DIFFRACTION100
2.47-2.540.30441340.26992735X-RAY DIFFRACTION99
2.54-2.610.30961250.2612754X-RAY DIFFRACTION100
2.61-2.70.36111320.26122768X-RAY DIFFRACTION100
2.7-2.80.3381510.25712732X-RAY DIFFRACTION100
2.8-2.910.31441890.25882690X-RAY DIFFRACTION100
2.91-3.040.29841590.25312742X-RAY DIFFRACTION100
3.04-3.20.31931770.24452750X-RAY DIFFRACTION100
3.2-3.40.26551270.23472761X-RAY DIFFRACTION100
3.4-3.660.2971430.22452776X-RAY DIFFRACTION100
3.66-4.030.28431390.20482801X-RAY DIFFRACTION100
4.03-4.610.22771010.18732835X-RAY DIFFRACTION100
4.61-5.810.22191040.20692881X-RAY DIFFRACTION100
5.82-72.620.24811480.24262969X-RAY DIFFRACTION100

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