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- PDB-4tzt: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ENOYL REDUCTASE (... -

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Basic information

Entry
Database: PDB / ID: 4tzt
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ENOYL REDUCTASE (INHA) COMPLEXED WITH N-(3-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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-468 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 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 10, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionAug 20, 2014ID: 2H7P
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._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 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5533
Polymers28,5551
Non-polymers9982
Water5,080282
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 area22210 Å2
ΔGint-138 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.782, 97.782, 141.125
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-608-

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-468 / (3S)-N-(3-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.: 282 / 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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 10% MPD, 50mM Na Citrate pH 6.5, 100 mM Hepes pH 7.2
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.86→42.341 Å / Num. obs: 33284 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.8
Reflection shellResolution: 1.86→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.86→42.34 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 1910 5.85 %random
Rwork0.1396 ---
obs0.1413 33284 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 67 282 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122131
X-RAY DIFFRACTIONf_angle_d1.3162908
X-RAY DIFFRACTIONf_dihedral_angle_d12.705797
X-RAY DIFFRACTIONf_chiral_restr0.057330
X-RAY DIFFRACTIONf_plane_restr0.007394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88450.23411440.22652313X-RAY DIFFRACTION100
1.8845-1.91030.21661390.19892277X-RAY DIFFRACTION100
1.9103-1.93760.23231480.18092282X-RAY DIFFRACTION100
1.9376-1.96650.1851480.16942292X-RAY DIFFRACTION100
1.9665-1.99720.1741440.16172326X-RAY DIFFRACTION100
1.9972-2.030.21961370.15952265X-RAY DIFFRACTION100
2.03-2.0650.19031470.15622292X-RAY DIFFRACTION100
2.065-2.10250.16671410.15032293X-RAY DIFFRACTION100
2.1025-2.1430.16221400.14742303X-RAY DIFFRACTION100
2.143-2.18670.15641440.14572289X-RAY DIFFRACTION100
2.1867-2.23430.17821430.13772318X-RAY DIFFRACTION100
2.2343-2.28620.14971350.1292308X-RAY DIFFRACTION100
2.2862-2.34340.15731450.12732273X-RAY DIFFRACTION100
2.3434-2.40670.18431380.12572281X-RAY DIFFRACTION100
2.4067-2.47760.18891460.12892298X-RAY DIFFRACTION100
2.4776-2.55750.18611430.14062308X-RAY DIFFRACTION100
2.5575-2.64890.19541390.13442312X-RAY DIFFRACTION100
2.6489-2.7550.17891400.13092291X-RAY DIFFRACTION100
2.755-2.88030.16971450.13432303X-RAY DIFFRACTION100
2.8803-3.03210.16821390.1342292X-RAY DIFFRACTION100
3.0321-3.2220.17531480.1412285X-RAY DIFFRACTION100
3.222-3.47070.1731420.14232293X-RAY DIFFRACTION100
3.4707-3.81980.16081460.13432304X-RAY DIFFRACTION100
3.8198-4.3720.14551430.12732294X-RAY DIFFRACTION100
4.372-5.50640.14171450.12392304X-RAY DIFFRACTION100
5.5064-42.35180.151380.14772273X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 45.5974 Å / Origin y: 48.1684 Å / Origin z: 52.5347 Å
111213212223313233
T0.1277 Å2-0.0043 Å2-0.0111 Å2-0.2186 Å20.0109 Å2--0.1636 Å2
L0.245 °2-0.0682 °20.1397 °2-0.2795 °20.0045 °2--0.44 °2
S-0.0224 Å °-0.0121 Å °0.0305 Å °0.0235 Å °-0.0122 Å °-0.0291 Å °-0.0533 Å °0.1409 Å °-0.014 Å °
Refinement TLS groupSelection details: all

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