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- PDB-7l00: Crystal Structure of C. difficile Enoyl-Acyl Carrier Protein Redu... -

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Basic information

Entry
Database: PDB / ID: 7l00
TitleCrystal Structure of C. difficile Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor
ComponentsEnoyl-Acyl Carrier Protein Reductase FabK
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Enoyl ACP reductase / Inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


nitronate monooxygenase / nitronate monooxygenase activity / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / dioxygenase activity
Similarity search - Function
Enoyl-(acyl-carrier-protein) reductase II, putative / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-XCJ / Enoyl-(Acyl-carrier-protein) reductase II
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAkhtar, A. / Santarsiero, B.D. / Hevener, K.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)IIRA- W 81XWH2010296 United States
CitationJournal: To be published
Title: Crystal Structure of C. difficile Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor
Authors: Jones, J.A. / Hevener, K.E. / Alghanim, L. / Akhtar, A. / Santarsiero, B.D.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Enoyl-Acyl Carrier Protein Reductase FabK
B: Enoyl-Acyl Carrier Protein Reductase FabK
C: Enoyl-Acyl Carrier Protein Reductase FabK
D: Enoyl-Acyl Carrier Protein Reductase FabK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,67022
Polymers132,8034
Non-polymers3,86818
Water12,809711
1
A: Enoyl-Acyl Carrier Protein Reductase FabK
B: Enoyl-Acyl Carrier Protein Reductase FabK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33511
Polymers66,4012
Non-polymers1,9349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-79 kcal/mol
Surface area23430 Å2
MethodPISA
2
C: Enoyl-Acyl Carrier Protein Reductase FabK
D: Enoyl-Acyl Carrier Protein Reductase FabK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33511
Polymers66,4012
Non-polymers1,9349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-79 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.900, 66.150, 101.780
Angle α, β, γ (deg.)90.000, 90.090, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Enoyl-Acyl Carrier Protein Reductase FabK / 2-nitropropane dioxygenase / Enoyl-(Acyl-carrier-protein) reductase II / Enoyl-[acyl-carrier- ...2-nitropropane dioxygenase / Enoyl-(Acyl-carrier-protein) reductase II / Enoyl-[acyl-carrier-protein] reductase FabK / Nitronate monooxygenase / Trans-2-enoyl-ACP reductase


Mass: 33200.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: fabK, BN1095_450087, BN1096_560086, BN1097_540088, cdgr_10495, E5F33_11835, E5F39_12870, E5F43_13130, FQN08_05765, SAMEA1402373_02260, SAMEA1402406_01811, SAMEA1402410_02165, SAMEA1710795_ ...Gene: fabK, BN1095_450087, BN1096_560086, BN1097_540088, cdgr_10495, E5F33_11835, E5F39_12870, E5F43_13130, FQN08_05765, SAMEA1402373_02260, SAMEA1402406_01811, SAMEA1402410_02165, SAMEA1710795_00230, SAMEA2239407_02705, SAMEA3374989_02524, SAMEA3375037_01248, SAMEA3375041_00754, SAMEA708418_02261
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A031WIF2, enoyl-[acyl-carrier-protein] reductase (NADH), nitronate monooxygenase

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Non-polymers , 5 types, 729 molecules

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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-XCJ / N-[6-(methylsulfonyl)-1,3-benzothiazol-2-yl]-2-[2-(1H-pyrrol-1-yl)-1,3-thiazol-4-yl]acetamide


Mass: 418.513 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H14N4O3S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.0M Tris(base) ;1.0M BICINE pH8.5, 25% PEG (w/v)3350 , 25% (v/v)PEG 1000, 25% (v/v) MPD, amino acids 0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine ...Details: 1.0M Tris(base) ;1.0M BICINE pH8.5, 25% PEG (w/v)3350 , 25% (v/v)PEG 1000, 25% (v/v) MPD, amino acids 0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→37.28 Å / Num. obs: 137306 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.1 / Num. measured all: 624006 / Scaling rejects: 137
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.72-1.753.90.5072637767020.7922.197.9
9.42-37.283.80.03733318730.98825.997

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6J

2z6j


Resolution: 1.72→36.69 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1851 6765 4.93 %
Rwork0.1444 130520 -
obs0.1463 137285 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.77 Å2 / Biso mean: 34.0976 Å2 / Biso min: 13.29 Å2
Refinement stepCycle: final / Resolution: 1.72→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9184 0 221 711 10116
Biso mean--26.27 41.89 -
Num. residues----1252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.740.25922120.19184314452697
1.74-1.760.21852050.16624307451299
1.76-1.780.18792000.1544295449598
1.78-1.80.22482480.15394236448499
1.8-1.830.20092510.15314315456699
1.83-1.850.21562380.16244290452899
1.85-1.880.19792710.14954287455899
1.88-1.910.23172410.14854250449199
1.91-1.940.21912020.14574351455399
1.94-1.970.19532130.14094313452699
1.97-20.19172400.13574326456699
2-2.040.19592390.136643204559100
2.04-2.080.20912260.14224321454799
2.08-2.120.20492150.14743314546100
2.12-2.170.19032260.14174359458599
2.17-2.220.17472090.13524341455099
2.22-2.270.20542330.140243484581100
2.27-2.330.18932850.143642714556100
2.33-2.40.19992110.14184376458799
2.4-2.480.1992100.139744034613100
2.48-2.570.17442340.144443454579100
2.57-2.670.17111970.145143664563100
2.67-2.790.20422240.149543824606100
2.79-2.940.20252530.164343764629100
2.94-3.120.18671990.15844344633100
3.12-3.370.20141980.157844014599100
3.37-3.70.17832480.148744054653100
3.7-4.240.17222320.13344174649100
4.24-5.340.1571880.128444924680100
5.34-36.690.14632170.13854548476599

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