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

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Basic information

Entry
Database: PDB / ID: 5cpb
TitleThe effect of isoleucine to alanine mutation on InhA enzyme crystallization pattern and inhibition by ligand PT70 (TCU)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Fatty acid biosynthesis inhibition
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 / 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: 1.997 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.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102864 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Protein plastic surgery
Authors: Li, H.-J.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

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)188,08512
Polymers184,1046
Non-polymers3,9816
Water9,638535
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: 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)125,3908
Polymers122,7364
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18920 Å2
ΔGint-124 kcal/mol
Surface area33950 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3908
Polymers122,7364
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area19190 Å2
ΔGint-125 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.319, 100.234, 379.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 30684.053 Da / Num. of mol.: 6 / Mutation: I215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: inhA, BN1213_03046, BN1303_01560, ERS024750_02142, ERS024751_00017, ERS024758_00017, ERS024764_00702, ERS094182_01549, ERS124362_00658, ERS124821_01119, ERS124823_00182, ERS124824_02080, ...Gene: inhA, BN1213_03046, BN1303_01560, ERS024750_02142, ERS024751_00017, ERS024758_00017, ERS024764_00702, ERS094182_01549, ERS124362_00658, ERS124821_01119, ERS124823_00182, ERS124824_02080, ERS124825_02290, ERS124826_03418, ERS124827_02051, ERS124828_01823, ERS124829_02123, ERS124830_01969, ERS124831_03317, ERS124832_00615, IQ38_05315, IQ40_05150, IQ42_05170, IQ45_05150, IQ47_05130, IQ48_05150, IU13_05205, IU15_05310, IU16_05150, IU17_05135, T209_05135
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.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsThe authors state that ligand PT70 (TCU) was the inhibitor ligand in the crystal, but was not ...The authors state that ligand PT70 (TCU) was the inhibitor ligand in the crystal, but was not included in the model due to disorder.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Sodium malonate, 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: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.997→50 Å / Num. obs: 106047 / % possible obs: 99.5 % / Redundancy: 6.8 % / Net I/σ(I): 24.5

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B37

2b37


Resolution: 1.997→48.734 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 5283 4.99 %
Rwork0.2 --
obs0.2024 105969 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.916 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6013 Å2-0 Å20 Å2
2---6.4894 Å20 Å2
3---7.0907 Å2
Refinement stepCycle: LAST / Resolution: 1.997→48.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11644 0 264 535 12443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812156
X-RAY DIFFRACTIONf_angle_d1.13616548
X-RAY DIFFRACTIONf_dihedral_angle_d16.4294571
X-RAY DIFFRACTIONf_chiral_restr0.0721841
X-RAY DIFFRACTIONf_plane_restr0.0052111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9967-2.01940.36171470.30853073X-RAY DIFFRACTION90
2.0194-2.04310.31461650.26713269X-RAY DIFFRACTION99
2.0431-2.0680.29281730.25143266X-RAY DIFFRACTION98
2.068-2.09420.31081680.26123414X-RAY DIFFRACTION100
2.0942-2.12180.32341710.24843284X-RAY DIFFRACTION100
2.1218-2.15080.28471630.22783391X-RAY DIFFRACTION100
2.1508-2.18160.28281770.22753341X-RAY DIFFRACTION100
2.1816-2.21410.29621600.22833342X-RAY DIFFRACTION100
2.2141-2.24870.2921540.21993380X-RAY DIFFRACTION100
2.2487-2.28560.26151780.21553355X-RAY DIFFRACTION100
2.2856-2.3250.24261950.20143366X-RAY DIFFRACTION100
2.325-2.36730.27521770.20073274X-RAY DIFFRACTION100
2.3673-2.41280.24781790.20193407X-RAY DIFFRACTION100
2.4128-2.4620.26491860.20673310X-RAY DIFFRACTION100
2.462-2.51560.28351680.233397X-RAY DIFFRACTION100
2.5156-2.57410.30961740.21873359X-RAY DIFFRACTION100
2.5741-2.63850.27241820.21183347X-RAY DIFFRACTION100
2.6385-2.70980.26341790.20043394X-RAY DIFFRACTION100
2.7098-2.78950.29041730.20443349X-RAY DIFFRACTION100
2.7895-2.87960.28151860.21513315X-RAY DIFFRACTION100
2.8796-2.98250.24431770.19953390X-RAY DIFFRACTION100
2.9825-3.10190.28671880.20343404X-RAY DIFFRACTION100
3.1019-3.2430.24831860.1953385X-RAY DIFFRACTION100
3.243-3.41390.25941890.19363384X-RAY DIFFRACTION100
3.4139-3.62780.20051790.18393366X-RAY DIFFRACTION100
3.6278-3.90780.23381700.18333383X-RAY DIFFRACTION99
3.9078-4.30080.20951910.17323370X-RAY DIFFRACTION98
4.3008-4.92260.21151650.16763346X-RAY DIFFRACTION98
4.9226-6.20.22951980.20173447X-RAY DIFFRACTION100
6.2-48.74840.20081850.1913578X-RAY DIFFRACTION99

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