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- PDB-4trn: STRUCTURE OF INHA FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED TO NADH -

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Basic information

Entry
Database: PDB / ID: 4trn
TitleSTRUCTURE OF INHA FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED TO NADH
ComponentsINHA
KeywordsOXIDOREDUCTASE / ENOYL ACP REDUCTASE
Function / homology
Function and homology information


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 / Short-chain dehydrogenase/reductase SDR / 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: 1.95 Å
AuthorsChollet, A. / Julien, S. / Mourey, L. / Maveyraud, L.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure of the enoyl-ACP reductase of Mycobacterium tuberculosis (InhA) in the apo-form and in complex with the active metabolite of isoniazid pre-formed by a biomimetic approach.
Authors: Chollet, A. / Mourey, L. / Lherbet, C. / Delbot, A. / Julien, S. / Baltas, M. / Bernadou, J. / Pratviel, G. / Maveyraud, L. / Bernardes-Genisson, V.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4935
Polymers28,5551
Non-polymers9384
Water2,360131
1
A: INHA
hetero molecules

A: INHA
hetero molecules

A: INHA
hetero molecules

A: INHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,97120
Polymers114,2194
Non-polymers3,75116
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 area22550 Å2
ΔGint-194 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.110, 98.110, 139.160
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 INHA


Mass: 28554.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inha / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P9WGR0, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / 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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 8-10 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium citrate, 0.1 M Na HEPES
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.95→49.06 Å / Num. all: 29499 / Num. obs: 29499 / % possible obs: 99.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 36.64 Å2 / Rsym value: 0.05 / Net I/σ(I): 29.24
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 3.99 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC2.10.0refinement
BUSTER-TNTphasing
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ENY

1eny


Resolution: 1.95→49.06 Å / Cor.coef. Fo:Fc: 0.9232 / Cor.coef. Fo:Fc free: 0.9301 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 1496 5.08 %RANDOM
Rwork0.1808 ---
obs0.1818 29470 99.83 %-
Displacement parametersBiso mean: 54.48 Å2
Baniso -1Baniso -2Baniso -3
1--11.1226 Å20 Å20 Å2
2---11.1226 Å20 Å2
3---22.2452 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 60 131 2201
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092137HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032930HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d728SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes332HARMONIC5
X-RAY DIFFRACTIONt_it2137HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion16.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2685SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.02 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2212 162 5.76 %
Rwork0.2253 2651 -
all0.225 2813 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 3.5037 Å / Origin y: -36.9909 Å / Origin z: 18.1042 Å
111213212223313233
T-0.221 Å20.0322 Å2-0.0044 Å2-0.206 Å20.016 Å2---0.1197 Å2
L0.5694 °20.0265 °20.0835 °2-0.3916 °2-0.0536 °2--2.8347 °2
S-0.0187 Å °0.0233 Å °0.0638 Å °-0.0071 Å °0.0369 Å °0.1041 Å °-0.264 Å °-1.0119 Å °-0.0182 Å °
Refinement TLS groupSelection details: { A|* }

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