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- PDB-2pr2: Structure of Mycobacterium tuberculosis enoyl-ACP reductase with ... -

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Basic information

Entry
Database: PDB / ID: 2pr2
TitleStructure of Mycobacterium tuberculosis enoyl-ACP reductase with bound INH-NADP.
Componentsenoyl-ACP ReductaseEnoyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / drug target of isoniazid
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
Chem-DG1 / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVetting, M.W. / Argyrou, A. / Blanchard, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: New insight into the mechanism of action of and resistance to isoniazid: interaction of Mycobacterium tuberculosis enoyl-ACP reductase with INH-NADP
Authors: Argyrou, A. / Vetting, M.W. / Blanchard, J.S.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Aug 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 / pdbx_struct_special_symmetry / 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-ACP Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4052
Polymers28,5551
Non-polymers8511
Water75742
1
A: enoyl-ACP Reductase
hetero molecules

A: enoyl-ACP Reductase
hetero molecules

A: enoyl-ACP Reductase
hetero molecules

A: enoyl-ACP Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6218
Polymers114,2194
Non-polymers3,4024
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-100 kcal/mol
Surface area33600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.128, 99.128, 139.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

DetailsThe biological assembly is monomeric and is contained within the assymetric unit.

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Components

#1: Protein enoyl-ACP Reductase / Enoyl-acyl carrier protein 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 / Plasmid: pET15b / 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-DG1 / (4S)-ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE / {(2R,3S,4R,5R)-5-[(4S)-3-(AMINOCARBONYL)-4-ISONICOTINOYLPYRIDIN-1(4H)-YL]-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL}METHYL [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 850.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N8O18P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: Cocrystallization with Inh-NADP at 4.8 mM 20 25% of 2-methyl-2,4-pentanediol, 100 mM Bicine pH 9.0., Vapour diffusion under oil, temperature 291K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2005
RadiationMonochromator: Rigaku Osmic Blue optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→41 Å / Num. all: 14562 / Num. obs: 14562 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.055 / Net I/σ(I): 36.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 7.5 / Num. unique all: 2077 / Rsym value: 0.353 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENY

1eny


Resolution: 2.5→41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.636 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.289 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 731 5 %RANDOM
Rwork0.184 ---
all0.185 14552 --
obs0.185 14552 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 56 42 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222088
X-RAY DIFFRACTIONr_angle_refined_deg1.6852.0042846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23423.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60915329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0781513
X-RAY DIFFRACTIONr_chiral_restr0.1370.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021563
X-RAY DIFFRACTIONr_nbd_refined0.2220.2948
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.212
X-RAY DIFFRACTIONr_mcbond_it0.5831.51350
X-RAY DIFFRACTIONr_mcangle_it0.98422103
X-RAY DIFFRACTIONr_scbond_it1.7933829
X-RAY DIFFRACTIONr_scangle_it2.894.5743
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 55 -
Rwork0.246 991 -
obs-1046 100 %
Refinement TLS params.Method: refined / Origin x: 3.648 Å / Origin y: -37.408 Å / Origin z: 18.167 Å
111213212223313233
T-0.1084 Å2-0.0103 Å2-0.0106 Å2-0.2018 Å2-0.0311 Å2---0.0521 Å2
L0.9351 °20.2257 °20.1195 °2-0.727 °20.1296 °2--1.3351 °2
S-0.038 Å °0.0869 Å °0.0636 Å °-0.0429 Å °-0.0481 Å °0.0501 Å °-0.1016 Å °-0.4923 Å °0.0861 Å °

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