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- PDB-5cp8: The effect of isoleucine to alanine mutation on InhA enzyme cryst... -

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Basic information

Entry
Database: PDB / ID: 5cp8
TitleThe effect of isoleucine to alanine mutation on InhA enzyme crystallization pattern and substrate binding loop conformation and flexibility
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Crystal packing Fatty acid biosynthesis Slow-onset inhibition Free energy calculation
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
Chem-ETE / 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: 2.4 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 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Other / Structure summary
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,0785
Polymers30,6841
Non-polymers1,3944
Water1,69394
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)128,31420
Polymers122,7364
Non-polymers5,57816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area19820 Å2
ΔGint-132 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.794, 99.794, 139.785
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-441-

HOH

21A-466-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 30684.053 Da / Num. of mol.: 1 / Mutation: I215A
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)

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Non-polymers , 5 types, 98 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C19H24O2
#4: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, magnesium chloride, PEG MME 550

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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: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16637 / % possible obs: 99.4 % / Redundancy: 16.1 % / Net I/σ(I): 28.7

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Processing

Software
NameClassification
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
RefinementResolution: 2.4→46.993 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 839 5.07 %
Rwork0.2056 --
obs0.2083 16559 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.128 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.7211 Å2-0 Å2-0 Å2
2--14.7211 Å2-0 Å2
3----29.4422 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 94 94 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082117
X-RAY DIFFRACTIONf_angle_d1.3712876
X-RAY DIFFRACTIONf_dihedral_angle_d21.551805
X-RAY DIFFRACTIONf_chiral_restr0.068315
X-RAY DIFFRACTIONf_plane_restr0.005364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55130.35271280.31442476X-RAY DIFFRACTION96
2.5513-2.74830.31650.25232550X-RAY DIFFRACTION100
2.7483-3.02480.28711420.23112579X-RAY DIFFRACTION100
3.0248-3.46240.32061280.20562620X-RAY DIFFRACTION100
3.4624-4.36180.19321400.16382654X-RAY DIFFRACTION100
4.3618-47.00190.24921360.19662841X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.2621 Å / Origin y: 15.4251 Å / Origin z: 5.4616 Å
111213212223313233
T0.2579 Å20.0744 Å2-0.0133 Å2-0.2709 Å2-0.0438 Å2--0.1923 Å2
L-0.3064 °20.1269 °2-0.0054 °2-1.0697 °2-0.0834 °2--0.4145 °2
S0.0062 Å °-0.0986 Å °-0.011 Å °0.2141 Å °-0.0814 Å °0.0615 Å °-0.2972 Å °-0.3491 Å °0.0629 Å °
Refinement TLS groupSelection details: all

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