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- PDB-3oey: Crystal structure of InhA_T266E:NADH complex -

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Basic information

Entry
Database: PDB / ID: 3oey
TitleCrystal structure of InhA_T266E:NADH complex
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-reductase
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NAD+) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...trans-2-enoyl-CoA reductase (NAD+) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMolle, V. / Gulten, G. / Vilcheze, C. / Veyron-Churlet, R. / Zanella-Cleon, I. / Sacchettini, J.C. / Jacobs Jr, W.R. / Kremer, L.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Phosphorylation of InhA inhibits mycolic acid biosynthesis and growth of Mycobacterium tuberculosis.
Authors: Molle, V. / Gulten, G. / Vilcheze, C. / Veyron-Churlet, R. / Zanella-Cleon, I. / Sacchettini, J.C. / Jacobs Jr, W.R. / Kremer, L.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,3643
Polymers28,5831
Non-polymers7822
Water3,243180
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)117,45812
Polymers114,3314
Non-polymers3,1268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area21070 Å2
ΔGint-188 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.154, 98.154, 139.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase


Mass: 28582.793 Da / Num. of mol.: 1 / Mutation: T266E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / Strain: H37Rv / Gene: inhA, MT1531, MTCY277.05, Rv1484 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM Hepes 7.2, 50 mM sodium citrate 6.5, 8-12% MPD, 4% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97947 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2→40.78 Å / Num. all: 27393 / Num. obs: 27393

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.78 Å / SU ML: 0.21 / σ(F): 0.14 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1335 5.04 %
Rwork0.1819 --
obs0.1835 26501 96.5 %
all-27393 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.311 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.9754 Å2-0 Å2-0 Å2
2--7.9754 Å2-0 Å2
3----15.9509 Å2
Refinement stepCycle: LAST / Resolution: 2→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 52 180 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072124
X-RAY DIFFRACTIONf_angle_d1.192896
X-RAY DIFFRACTIONf_dihedral_angle_d14.432790
X-RAY DIFFRACTIONf_chiral_restr0.083327
X-RAY DIFFRACTIONf_plane_restr0.004374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.07180.28131350.21642314X-RAY DIFFRACTION92
2.0718-2.15470.23081290.21192367X-RAY DIFFRACTION93
2.1547-2.25280.26731100.19092462X-RAY DIFFRACTION95
2.2528-2.37160.26181380.20762442X-RAY DIFFRACTION96
2.3716-2.52010.23631220.20362495X-RAY DIFFRACTION97
2.5201-2.71470.25771400.19222514X-RAY DIFFRACTION97
2.7147-2.98780.2441420.19832556X-RAY DIFFRACTION98
2.9878-3.41990.22971550.19122566X-RAY DIFFRACTION99
3.4199-4.3080.17621430.15912645X-RAY DIFFRACTION99
4.308-40.78980.1671210.16172805X-RAY DIFFRACTION98

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