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- PDB-4u0k: Crystal structure of Mycobacterium tuberculosis enoyl reductase c... -

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Basic information

Entry
Database: PDB / ID: 4u0k
TitleCrystal structure of Mycobacterium tuberculosis enoyl reductase complexed with N-(5-chloro-2-methylphenyl)-1-cyclohexyl-5-oxopyrrolidine-3-carboxamide
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / pyrrolidine carboxamide
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 / 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
Chem-744 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHe, X. / Alian, A. / Stroud, R.M. / Ortiz de Montellano, P.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56531 United States
CitationJournal: J. Med. Chem. / Year: 2006
Title: Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis
Authors: He, X. / Alian, A. / Stroud, R.M. / Ortiz de Montellano, P.R.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJul 30, 2014ID: 2H7N
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 25, 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 / refine_hist
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)29,5533
Polymers28,5551
Non-polymers9982
Water4,846269
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)118,21212
Polymers114,2194
Non-polymers3,9938
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area21970 Å2
ΔGint-132 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.057, 97.057, 140.421
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-636-

HOH

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-gold (DE3)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-744 / (3S)-N-(5-CHLORO-2-METHYLPHENYL)-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE


Mass: 334.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23ClN2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 6% MPD, 50 mM Na Citrate pH 6.5, 100mM Hepes pH 8.0
PH range: 7 - 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2006
RadiationMonochromator: double flat, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.9→41 Å / Num. obs: 30670 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.6 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CNSphasing
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1P45

1p45


Resolution: 1.9→40.894 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 15.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1729 2335 7.61 %random
Rwork0.1438 ---
obs0.146 30665 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→40.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 67 269 2325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112127
X-RAY DIFFRACTIONf_angle_d1.2582902
X-RAY DIFFRACTIONf_dihedral_angle_d12.781794
X-RAY DIFFRACTIONf_chiral_restr0.052328
X-RAY DIFFRACTIONf_plane_restr0.007393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93890.19481330.16611572X-RAY DIFFRACTION94
1.9389-1.98110.23211220.15531613X-RAY DIFFRACTION96
1.9811-2.02720.18951240.15941633X-RAY DIFFRACTION98
2.0272-2.07790.19771370.14991613X-RAY DIFFRACTION97
2.0779-2.1340.18741260.14831627X-RAY DIFFRACTION97
2.134-2.19680.18551300.14451641X-RAY DIFFRACTION97
2.1968-2.26770.15321480.1361605X-RAY DIFFRACTION97
2.2677-2.34880.17241430.1331637X-RAY DIFFRACTION97
2.3488-2.44280.17981320.13121651X-RAY DIFFRACTION97
2.4428-2.5540.16731380.14651662X-RAY DIFFRACTION98
2.554-2.68860.18851330.13981648X-RAY DIFFRACTION98
2.6886-2.8570.18031520.14091670X-RAY DIFFRACTION98
2.857-3.07750.22651450.14881677X-RAY DIFFRACTION99
3.0775-3.38710.13781680.1521682X-RAY DIFFRACTION99
3.3871-3.87690.15671500.13541739X-RAY DIFFRACTION100
3.8769-4.88320.15061240.12471789X-RAY DIFFRACTION99
4.8832-40.90330.18161300.16611871X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 45.5857 Å / Origin y: 47.9713 Å / Origin z: 52.1419 Å
111213212223313233
T0.106 Å2-0.0039 Å2-0.0104 Å2-0.1745 Å20.0048 Å2--0.1419 Å2
L0.2332 °2-0.0288 °20.1955 °2-0.4566 °2-0.0114 °2--0.4661 °2
S-0.0246 Å °-0.0049 Å °0.0289 Å °0.0227 Å °-0.0064 Å °-0.0661 Å °-0.043 Å °0.1302 Å °0.0325 Å °
Refinement TLS groupSelection details: all

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