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- PDB-5coq: The effect of valine to alanine mutation on InhA enzyme crystalli... -

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Basic information

Entry
Database: PDB / ID: 5coq
TitleThe effect of valine to alanine mutation on InhA enzyme crystallization pattern and substrate binding loop conformation and flexibility
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Fatty acid biosynthesis Slow-onset inhibition Crystallographic disorder Molecular dynamics simulation
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 / 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 / 5-HEXYL-2-(2-METHYLPHENOXY)PHENOL / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsLi, H.-J. / Lai, C.-T. / Liu, N. / Yu, W. / Shah, S. / Bommineni, G.R. / Perrone, V. / Garcia-Diaz, M. / Tonge, P.J. / Simmerling, C.
CitationJournal: Biochemistry / Year: 2015
Title: Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.
Authors: Lai, C.T. / Li, H.J. / Yu, W. / Shah, S. / Bommineni, G.R. / Perrone, V. / Garcia-Diaz, M. / Tonge, P.J. / Simmerling, C.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,60713
Polymers122,7924
Non-polymers3,8149
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19050 Å2
ΔGint-139 kcal/mol
Surface area32690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.095, 91.903, 102.846
Angle α, β, γ (deg.)90.00, 106.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 30698.080 Da / Num. of mol.: 4 / Mutation: V203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Production host: Escherichia coli (E. coli)
References: UniProt: M9TGV3, 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.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-TCU / 5-HEXYL-2-(2-METHYLPHENOXY)PHENOL / 2-(O-TOLYLOXY)-5-HEXYLPHENOL


Mass: 284.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H24O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Potassium sodium tartrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48995 / % possible obs: 98.5 % / Redundancy: 7.6 % / Net I/σ(I): 21.9

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Processing

Software
NameVersionClassification
CBASS1.8.4_1496data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.4_1496refinement
RefinementResolution: 2.3→46.067 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 2478 5.06 %
Rwork0.1606 --
obs0.1632 48995 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 261 328 8397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088237
X-RAY DIFFRACTIONf_angle_d1.1311210
X-RAY DIFFRACTIONf_dihedral_angle_d15.7032970
X-RAY DIFFRACTIONf_chiral_restr0.0411275
X-RAY DIFFRACTIONf_plane_restr0.0051421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.34460.26611130.20672267X-RAY DIFFRACTION87
2.3446-2.39250.25731340.19982545X-RAY DIFFRACTION98
2.3925-2.44450.26981310.2082611X-RAY DIFFRACTION98
2.4445-2.50140.30721600.20792541X-RAY DIFFRACTION98
2.5014-2.56390.27091460.22543X-RAY DIFFRACTION98
2.5639-2.63320.26191210.19022618X-RAY DIFFRACTION98
2.6332-2.71070.29741320.18632606X-RAY DIFFRACTION98
2.7107-2.79820.24781490.18462554X-RAY DIFFRACTION98
2.7982-2.89820.22371270.17812589X-RAY DIFFRACTION98
2.8982-3.01420.22411330.17642618X-RAY DIFFRACTION98
3.0142-3.15140.24911390.1832589X-RAY DIFFRACTION99
3.1514-3.31750.24241530.17382597X-RAY DIFFRACTION99
3.3175-3.52520.2121550.16182599X-RAY DIFFRACTION99
3.5252-3.79730.2051340.15072606X-RAY DIFFRACTION99
3.7973-4.17920.16971350.13852641X-RAY DIFFRACTION99
4.1792-4.78340.1641530.12392608X-RAY DIFFRACTION99
4.7834-6.02450.1961410.14842675X-RAY DIFFRACTION100
6.0245-46.07610.17661220.1462710X-RAY DIFFRACTION99

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