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- PDB-3oew: Crystal structure of wild-type InhA:NADH complex -

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Basic information

Entry
Database: PDB / ID: 3oew
TitleCrystal structure of wild-type InhA:NADH complex
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoly-reductase
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,3363
Polymers28,5551
Non-polymers7822
Water3,081171
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)117,34612
Polymers114,2194
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 area20890 Å2
ΔGint-194 kcal/mol
Surface area33570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.551, 98.551, 139.714
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

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Components

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


Mass: 28554.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / 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.: 171 / 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: 3.5 Å3/Da / Density % sol: 64.85 %
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: 2.1→40.88 Å / Num. all: 23240 / Num. obs: 23240

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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: 2.2→40.88 Å / SU ML: 0.25 / σ(F): 0.11 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 1014 5.14 %
Rwork0.1667 --
obs0.1688 19722 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.811 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6669 Å2-0 Å2-0 Å2
2--3.6669 Å2-0 Å2
3----7.3338 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 52 171 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082126
X-RAY DIFFRACTIONf_angle_d1.2112902
X-RAY DIFFRACTIONf_dihedral_angle_d14.699792
X-RAY DIFFRACTIONf_chiral_restr0.078330
X-RAY DIFFRACTIONf_plane_restr0.004373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.31610.3151320.22342517X-RAY DIFFRACTION91
2.3161-2.46120.25311510.20332600X-RAY DIFFRACTION93
2.4612-2.65120.2671460.19662649X-RAY DIFFRACTION95
2.6512-2.91790.23921360.18262699X-RAY DIFFRACTION95
2.9179-3.340.22391600.17192705X-RAY DIFFRACTION96
3.34-4.20740.16531350.14652743X-RAY DIFFRACTION95
4.2074-40.88820.18531540.14792795X-RAY DIFFRACTION91

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