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- PDB-7u0o: Crystal structure of an enoyl-[acyl-carrier-protein] reductase In... -

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Basic information

Entry
Database: PDB / ID: 7u0o
TitleCrystal structure of an enoyl-[acyl-carrier-protein] reductase InhA from Mycobacterium fortuitum bound to NAD and NITD-916
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / Mycobacterium / pulmonary infection / CF / NAD-depdendent enzyme / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


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 / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-3KY / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycolicibacterium fortuitum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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: Antimicrob.Agents Chemother. / Year: 2023
Title: In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum.
Authors: Roquet-Baneres, F. / Alcaraz, M. / Hamela, C. / Abendroth, J. / Edwards, T.E. / Kremer, L.
History
DepositionFeb 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 25, 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)60,88010
Polymers58,8142
Non-polymers2,0678
Water4,486249
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)121,76020
Polymers117,6274
Non-polymers4,13316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area19300 Å2
ΔGint-201 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 101.540, 76.480
Angle α, β, γ (deg.)90.000, 114.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21B-434-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29406.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium fortuitum (bacteria)
Gene: fabI, inhA, A5637_21995, A5751_12770, FKW78_11710, NCTC1542_01491, XA26_29600
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0N9XSE6, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 257 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MyfoA.00170.a.B1.PS38584 at 19 mg/mL with 3.5 mM NAD and 3.5 mM NITD-916 against JCSG+ screen condition A11, 0.2 M ammonium dihydrogen phosphate, 0.1 M Tris pH 8.5, 50% MPD, crystal tracking ...Details: MyfoA.00170.a.B1.PS38584 at 19 mg/mL with 3.5 mM NAD and 3.5 mM NITD-916 against JCSG+ screen condition A11, 0.2 M ammonium dihydrogen phosphate, 0.1 M Tris pH 8.5, 50% MPD, crystal tracking ID 323553a11, unique puck ID jrh6-3

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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: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→39.38 Å / Num. obs: 34582 / % possible obs: 99.6 % / Redundancy: 3.57 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 0.93 / Net I/σ(I): 13.32 / Num. measured all: 123465 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.13.5910.3913.325550.8920.46299.8
2.1-2.163.6020.333.9325110.9240.38999.6
2.16-2.223.5850.2624.9424290.9440.30999.7
2.22-2.293.6040.2335.6223260.9560.274100
2.29-2.373.6010.1926.5622640.9750.22699.6
2.37-2.453.5990.1687.3921840.9830.19899.6
2.45-2.543.5940.1627.7721640.980.19199.7
2.54-2.653.5880.1379.1920290.9840.16199.7
2.65-2.763.5820.10811.0719470.9890.12899.9
2.76-2.93.5850.08813.3218920.9930.10499.7
2.9-3.063.5740.07515.0118000.9950.08999.4
3.06-3.243.540.05618.8516800.9970.06699.6
3.24-3.473.530.04921.6815890.9970.058100
3.47-3.743.5090.0425.3214770.9980.04899.1
3.74-4.13.5190.03728.1413610.9980.04499.1
4.1-4.583.4960.03229.7312370.9980.03899.7
4.58-5.293.5410.02930.9510970.9990.03499.5
5.29-6.483.5320.03229.299290.9980.03899.3
6.48-9.173.5530.02733.147180.9990.03199.9
9.17-39.383.3690.02734.753930.9980.03395.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.20_4438refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7k73

7k73


Resolution: 2.05→39.38 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2035 5.89 %
Rwork0.2048 32520 -
obs0.2073 34555 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.38 Å2 / Biso mean: 34.5275 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: final / Resolution: 2.05→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 138 257 4258
Biso mean--29.36 35.24 -
Num. residues----536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10.27341430.25421822325100
2.1-2.150.31451480.245621592307100
2.15-2.210.30651170.242421532270100
2.21-2.270.28281390.232721502289100
2.27-2.350.33681190.236621792298100
2.35-2.430.26081570.22321082265100
2.43-2.530.26331310.226421662297100
2.53-2.640.26311400.222921912331100
2.64-2.780.27781190.22621762295100
2.78-2.960.24311520.215921522304100
2.96-3.180.25171360.212121582294100
3.18-3.50.22841420.202821672309100
3.5-4.010.23081220.175521942316100
4.01-5.050.20811240.165421842308100
5.05-39.380.22541460.1982201234799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9772-0.24360.38572.423-0.72631.03960.14090.81550.2922-0.356-0.03080.0409-0.0512-0.1077-0.04320.34260.0470.03610.59820.19840.254929.3621-2.34457.6378
20.033-0.0427-0.01390.1610.15140.17610.06210.38080.3956-0.23390.01330.0583-0.16020.01520.02380.44120.06240.08170.54410.39940.638926.49979.38119.5249
31.2689-0.0716-0.28511.4108-0.19561.64940.09590.31830.5107-0.0846-0.0224-0.011-0.10820.0046-0.01080.20280.01840.04640.18590.07950.270224.77890.98725.8398
42.1932-0.0636-0.68393.3312-0.9311.36120.1965-0.11130.2646-0.0316-0.1137-0.4461-0.18710.1294-0.08490.29340.02290.09460.2110.04660.232736.3713-3.145421.6784
50.1665-0.5575-0.80881.89932.75233.9880.2568-0.1972-0.34680.55670.1165-1.5022-0.40480.9067-0.36340.5565-0.1133-0.2120.42510.07590.707546.856-9.943328.252
62.00910.2982-0.26832.14580.10550.158-0.07710.570.1675-0.2287-0.0324-0.0887-0.12370.05090.10220.22760.01070.00540.29030.02080.11430.4934-13.888118.3656
70.7369-0.40650.04290.28920.15410.49610.05330.6136-0.5162-0.28230.00420.01370.1451-0.05440.15560.36270.0098-0.03640.6033-0.36020.423817.9028-36.1258.5016
80.9614-0.1837-1.19054.01430.70221.8231-0.09030.1344-0.1911-0.15770.071-0.10780.56850.1066-0.00690.35440.0864-0.09970.4858-0.37470.679130.3399-44.98811.7939
92.33120.2244-1.61551.9486-0.93893.3488-0.09370.4883-0.781-0.0923-0.0448-0.00630.2643-0.29850.19140.1902-0.0131-0.06320.2674-0.11720.366318.2908-36.976225.3794
101.81560.15380.37731.8740.33690.90360.03370.3286-0.4931-0.0562-0.0598-0.05090.03250.02270.05310.1910.016-0.02470.1708-0.07270.250524.7668-32.179926.0574
112.8968-0.097-0.31033.40951.01692.32190.1882-0.1145-0.2179-0.0402-0.19170.58570.128-0.3015-0.01530.29460.0285-0.08830.2332-0.02450.255811.3332-29.554621.5895
121.9551.51530.84842.92860.17130.5020.1593-0.0126-0.25430.6292-0.23621.13130.4476-0.57970.02750.3934-0.06520.09630.368-0.09250.49283.1055-21.326124.4643
131.48620.09750.62351.7801-0.46040.4410.03860.642-0.1636-0.1729-0.09230.0204-0.0077-0.07780.02720.23950.0179-0.01250.313-0.01340.122220.6149-18.519818.4598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 82 )A32 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 182 )A83 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 208 )A183 - 208
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 225 )A209 - 225
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 269 )A226 - 269
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 67 )B2 - 67
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 82 )B68 - 82
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 112 )B83 - 112
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 182 )B113 - 182
11X-RAY DIFFRACTION11chain 'B' and (resid 183 through 208 )B183 - 208
12X-RAY DIFFRACTION12chain 'B' and (resid 209 through 235 )B209 - 235
13X-RAY DIFFRACTION13chain 'B' and (resid 236 through 269 )B236 - 269

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