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- PDB-2idz: Crystal structure of wild type Enoyl-ACP(CoA) reductase from Myco... -

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Basic information

Entry
Database: PDB / ID: 2idz
TitleCrystal structure of wild type Enoyl-ACP(CoA) reductase from Mycobacterium tuberculosis in complex with NADH-INH
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / ENOYL-ACYL CARRIER PROTEIN / InhA / INH / isoniazid
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 [NAD(P)H] activity / 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
Chem-ZID / 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 Å
AuthorsDias, M.V.B. / Prado, M.P.X. / Vasconcelos, I.B. / Valmir, F. / Basso, L.A. / Santos, D.S. / Azevedo Jr., W.F.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Crystallographic studies on the binding of isonicotinyl-NAD adduct to wild-type and isoniazid resistant 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis.
Authors: Dias, M.V. / Vasconcelos, I.B. / Prado, A.M. / Fadel, V. / Basso, L.A. / de Azevedo, W.F. / Santos, D.S.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)29,1922
Polymers28,4241
Non-polymers7691
Water4,270237
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)116,7688
Polymers113,6944
Non-polymers3,0744
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 area19700 Å2
ΔGint-129 kcal/mol
Surface area32170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.093, 97.093, 136.939
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-335-

HOH

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Components

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


Mass: 28423.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Plasmid: PET-23D(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-ZID / ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE


Mass: 768.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N8O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05M SODIUM CITRATE, 0.05M HEPES, 8-15% 2-METHYL-2-4-PENTANEDIOL (MPD), PH 7.2, TEMPERATURE 293K , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 22, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2→40.193 Å / Num. obs: 26409 / % possible obs: 96.11 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098 / Rsym value: 0.094 / Net I/σ(I): 5.2
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3795 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZID

1zid


Resolution: 2→40.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.5 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.145 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1338 5.1 %RANDOM
Rwork0.18793 ---
all0.18983 26409 --
obs0.1898 25045 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.205 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 52 237 2283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222089
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9992846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0365267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03623.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9621513
X-RAY DIFFRACTIONr_chiral_restr0.1750.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021563
X-RAY DIFFRACTIONr_nbd_refined0.2680.21345
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.2130
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.236
X-RAY DIFFRACTIONr_mcbond_it1.2241.51366
X-RAY DIFFRACTIONr_mcangle_it1.74922110
X-RAY DIFFRACTIONr_scbond_it2.9573837
X-RAY DIFFRACTIONr_scangle_it4.3594.5736
LS refinement shellResolution: 2→2.052 Å
RfactorNum. reflection% reflection
Rfree0.332 83 -
Rwork0.314 --
obs--100 %

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