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- PDB-4trm: Structure of the apo form of InhA from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4trm
TitleStructure of the apo form of InhA from Mycobacterium tuberculosis
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / ENOYL 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
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5247
Polymers171,3296
Non-polymers1951
Water14,304794
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)114,6106
Polymers114,2194
Non-polymers3902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14100 Å2
ΔGint-95 kcal/mol
Surface area35330 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)114,2194
Polymers114,2194
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14080 Å2
ΔGint-98 kcal/mol
Surface area32760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.096, 81.787, 187.242
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 269 / Label seq-ID: 3 - 269

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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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.: 6
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % (W/V) PEG 400 0.1 M sodium acetate 0.1 M Na-MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.8→46.98 Å / Num. all: 136543 / Num. obs: 136543 / % possible obs: 98 % / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 12.55
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.49 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
BUSTER-TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2B35

2b35


Resolution: 1.8→35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.519 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21905 6889 5 %RANDOM
Rwork0.18885 ---
obs0.19035 136543 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.636 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å21.27 Å2
2---1.3 Å2-0 Å2
3---3.28 Å2
Refinement stepCycle: 1 / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11118 0 12 794 11924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911539
X-RAY DIFFRACTIONr_bond_other_d0.0110.0211020
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.96515731
X-RAY DIFFRACTIONr_angle_other_deg1.594325225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03651556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89524.063411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.584151725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0561557
X-RAY DIFFRACTIONr_chiral_restr0.1080.21823
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113365
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022504
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6684.0166236
X-RAY DIFFRACTIONr_mcbond_other4.6664.0146235
X-RAY DIFFRACTIONr_mcangle_it5.365.7017788
X-RAY DIFFRACTIONr_mcangle_other5.365.7037789
X-RAY DIFFRACTIONr_scbond_it7.1675.5835303
X-RAY DIFFRACTIONr_scbond_other7.1575.5845303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6277.3657944
X-RAY DIFFRACTIONr_long_range_B_refined11.38614.60513663
X-RAY DIFFRACTIONr_long_range_B_other11.39713.49613326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A143620.07
12B143620.07
21A139050.09
22C139050.09
31A137540.09
32D137540.09
41A140190.1
42E140190.1
51A133070.09
52F133070.09
61B141000.08
62C141000.08
71B137750.08
72D137750.08
81B138900.1
82E138900.1
91B133130.08
92F133130.08
101C135340.09
102D135340.09
111C135270.1
112E135270.1
121C130580.09
122F130580.09
131D134360.09
132E134360.09
141D128310.09
142F128310.09
151E131410.11
152F131410.11
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 450 -
Rwork0.417 7938 -
obs--81.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4497-0.20080.0180.2898-0.01411.5104-0.0002-0.15990.32410.1225-0.0381-0.124-0.14130.11990.03830.2771-0.0263-0.10460.2346-0.02120.117215.19943.132715.6361
21.84160.05310.3820.4675-0.06781.25470.00140.3379-0.065-0.1409-0.0399-0.13260.14950.22670.03850.28230.0359-0.03730.29680.00670.068114.9149-5.0206-15.7108
31.16310.26210.54941.96190.25792.4849-0.06630.55480.0868-0.13190.1283-0.3591-0.13910.898-0.06190.3312-0.0746-0.0710.64710.02590.111747.63255.252444.8205
41.35210.26980.03011.3647-0.09322.9602-0.1643-0.00920.44510.03260.00440.1721-0.7039-0.35670.15980.46530.0547-0.14350.2377-0.00540.180328.316121.511464.7597
51.18430.30280.5971.60430.25122.71860.1825-0.4863-0.04140.333-0.0976-0.04530.4551-0.4931-0.0850.5078-0.1324-0.12830.46010.03380.03426.9718-4.504281.175
61.4680.70880.3211.28340.14123.3490.27220.1135-0.32490.08870.0178-0.04450.9429-0.0003-0.290.5826-0.0134-0.21060.2212-0.0290.125932.0566-19.369653.5791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 269
2X-RAY DIFFRACTION2B3 - 269
3X-RAY DIFFRACTION3C3 - 269
4X-RAY DIFFRACTION4D3 - 269
5X-RAY DIFFRACTION5E3 - 269
6X-RAY DIFFRACTION6F3 - 269

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