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- PDB-7u0m: Crystal structure of a enoyl-[acyl-carrier-protein] reductase (In... -

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Basic information

Entry
Database: PDB / ID: 7u0m
TitleCrystal structure of a enoyl-[acyl-carrier-protein] reductase (InhA) from Mycobacterium abscessus bound to NAD and NITD-916
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / Mycobacterium / tuberculosis / cystic fibrosis / CF / pulmonary infections / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-3KY / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA.
Authors: Alcaraz, M. / Roquet-Baneres, F. / Leon-Icaza, S.A. / Abendroth, J. / Boudehen, Y.M. / Cougoule, C. / Edwards, T.E. / Kremer, L.
History
DepositionFeb 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3868
Polymers59,3902
Non-polymers1,9966
Water12,016667
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,77216
Polymers118,7804
Non-polymers3,99112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area19300 Å2
ΔGint-173 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.310, 102.310, 76.820
Angle α, β, γ (deg.)90.000, 114.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-623-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29695.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: MAB_2722c / Production host: Escherichia coli (E. coli)
References: UniProt: B1MC30, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-3KY / 6-[(4,4-dimethylcyclohexyl)methyl]-4-hydroxy-3-phenylpyridin-2(1H)-one


Mass: 311.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 48.05 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyabA.00170.a.B1.PS38577 at 23.06 mg/mL with 3.5 mM NAD and 3.5 mM NITD-916 against the Index Screen condition H10: 0.2 M sodium citrate tribasic, 20% ethylene glycol supplemented with ...Details: MyabA.00170.a.B1.PS38577 at 23.06 mg/mL with 3.5 mM NAD and 3.5 mM NITD-916 against the Index Screen condition H10: 0.2 M sodium citrate tribasic, 20% ethylene glycol supplemented with compounds as cryo-protectant, crystal ID 323195h10, unique puck ID tdn4-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→41.32 Å / Num. obs: 95830 / % possible obs: 98.2 % / Redundancy: 3.949 % / Biso Wilson estimate: 11.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.053 / Χ2: 0.975 / Net I/σ(I): 18.13 / Num. measured all: 378452
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.492.6810.2284.2916187715560370.9330.28584.4
1.49-1.533.0330.1775.9920210705666630.9640.21594.4
1.53-1.573.7460.1597.8425546685068190.9780.18599.5
1.57-1.624.1330.1399.4727301661566050.9850.1699.8
1.62-1.674.1310.11810.7926479642164100.9890.13699.8
1.67-1.734.1450.10312.425591618361740.990.11999.9
1.73-1.84.1440.08814.3424867602260010.9910.10299.7
1.8-1.874.1560.07416.7923881576257460.9940.08599.7
1.87-1.964.1460.06319.3622946555055340.9950.07399.7
1.96-2.054.1450.05521.5221859528752740.9960.06499.8
2.05-2.164.1570.0524.120840502750130.9960.05799.7
2.16-2.294.1450.04625.9419876481747950.9970.05299.5
2.29-2.454.1560.04227.5418492446344490.9970.04899.7
2.45-2.654.1610.0428.6817425419641880.9970.04699.8
2.65-2.94.1780.03829.9916027385138360.9970.04499.6
2.9-3.244.1760.03631.6814532349334800.9980.04299.6
3.24-3.744.1490.03632.7412701306330610.9970.04299.9
3.74-4.594.1690.03433.7810924263526200.9980.03999.4
4.59-6.484.1660.03433.658402202720170.9980.03999.5
6.48-41.323.940.03833.074366113011080.9970.04498.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20_4438refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7l6c

7l6c


Resolution: 1.45→41.32 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1787 1989 2.08 %
Rwork0.1505 93833 -
obs0.1511 95822 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.5 Å2 / Biso mean: 17.0017 Å2 / Biso min: 5.44 Å2
Refinement stepCycle: final / Resolution: 1.45→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 136 693 4809
Biso mean--10.72 31.51 -
Num. residues----534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.490.26661220.19545682580484
1.49-1.530.21021330.16546426655994
1.53-1.570.22291290.151768136942100
1.57-1.620.20531530.145767626915100
1.62-1.680.17941430.145867826925100
1.68-1.750.17221670.149368036970100
1.75-1.830.21151330.152768116944100
1.83-1.920.17541350.146267766911100
1.92-2.040.17451220.149967926914100
2.04-2.20.171460.14968266972100
2.2-2.420.17431530.14568036956100
2.42-2.770.19241510.155968236974100
2.77-3.490.18171440.148668506994100
3.49-41.320.15061580.148468847042100

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