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- PDB-2ntv: Mycobacterium leprae InhA bound with PTH-NAD adduct -

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Basic information

Entry
Database: PDB / ID: 2ntv
TitleMycobacterium leprae InhA bound with PTH-NAD adduct
ComponentsEnoyl-[ACP] reductase
KeywordsOXIDOREDUCTASE / leprosy / InhA / prothionamide
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
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-P1H / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, F. / Sacchettini, J.C.
CitationJournal: J.Exp.Med. / Year: 2007
Title: Mechanism of thioamide drug action against tuberculosis and leprosy.
Authors: Wang, F. / Langley, R. / Gulten, G. / Dover, L.G. / Besra, G.S. / Jacobs, W.R. / Sacchettini, J.C.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[ACP] reductase
B: Enoyl-[ACP] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8314
Polymers57,2052
Non-polymers1,6252
Water3,657203
1
A: Enoyl-[ACP] reductase
B: Enoyl-[ACP] reductase
hetero molecules

A: Enoyl-[ACP] reductase
B: Enoyl-[ACP] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6618
Polymers114,4114
Non-polymers3,2504
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area20370 Å2
ΔGint-93 kcal/mol
Surface area34350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.232, 100.019, 186.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-458-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit

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Components

#1: Protein Enoyl-[ACP] reductase


Mass: 28602.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Gene: inhA / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9CBM1
#2: Chemical ChemComp-P1H / {(2R,3S,4R,5R)-5-[(4S)-3-(AMINOCARBONYL)-4-(2-PROPYLISONICOTINOYL)PYRIDIN-1(4H)-YL]-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL}M ETHYL [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE / 2-PROPYL-ISONICOTINIC-ACYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE


Mass: 812.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H38N8O15P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% MPD, 4% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 121 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49856 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Χ2: 1.145 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2 / Num. unique all: 4735 / Rsym value: 0.88 / Χ2: 0.885 / % possible all: 95.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZID

1zid


Resolution: 2.1→19.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2527 5.1 %RANDOM
Rwork0.219 ---
obs0.22 49775 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.098 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 110 203 4329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224208
X-RAY DIFFRACTIONr_angle_refined_deg2.14625726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3455534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94324.321162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.48515680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1791524
X-RAY DIFFRACTIONr_chiral_restr0.3190.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023214
X-RAY DIFFRACTIONr_nbd_refined0.2580.22211
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2129
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.220
X-RAY DIFFRACTIONr_mcbond_it0.6481.52648
X-RAY DIFFRACTIONr_mcangle_it1.22424224
X-RAY DIFFRACTIONr_scbond_it1.94831560
X-RAY DIFFRACTIONr_scangle_it3.0924.51502
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 193 -
Rwork0.304 3186 -
obs-3379 93.34 %

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