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

Basic information

• Entry: Database: PDB / ID: 4tzt
• Title: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ENOYL REDUCTASE (INHA) COMPLEXED WITH N-(3-CHLORO-2-METHYLPHENYL)-1-CYCLOHEXYL- 5-OXOPYRROLIDINE-3-CARBOXAMIDE
• Components: Enoyl-[acyl-carrier-protein] reductase [NADH]
• Keywords: OXIDOREDUCTASE / pyrrolidine carboxamide

Function / homology

Function:

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

Domain/homology:

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

Component:

Chem-468 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]

• Biological species: Mycobacterium tuberculosis (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å
• Authors: He, X. / Alian, A. / Stroud, R.M. / Ortiz de Montellano, P.R.

Funding support

United States, 1items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM56531	United States

• Citation: Journal: 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

Deposition	Jul 10, 2014	Deposition site: RCSB / Processing site: RCSB
Supersession	Aug 20, 2014	ID: 2H7P
Revision 1.0	Aug 20, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy Category: 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 / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

Summary:

• 29.6 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	29,553	3
Polymers	28,555	1
Non-polymers	998	2
Water	5,080	282

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

Summary:

• defined by author&software
• 118 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	118,212	12
Polymers	114,219	4
Non-polymers	3,993	8
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_665	-x+1,-y+1,z	1
crystal symmetry operation	7_555	y,x,-z+2/3	1
crystal symmetry operation	10_665	-y+1,-x+1,-z+2/3	1

Calculated values:

Buried area	22210 Å2
ΔGint	-138 kcal/mol
Surface area	33720 Å2
Method	PISA

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 number	180
Space group name H-M	P6222

Components on special symmetry positions

ID	Model	Components
1	1	A-608- HOH

Components

#1: Protein

A Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase

Details:

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

A-500 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide

Details:

Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

#3: Chemical

A-501 ChemComp-468 / (3S)-N-(3-CHLORO-2-METHYLPHENYL)-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE

Details:

Mass: 334.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₂₃ClN₂O₂

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 3.39 ų/Da / Density % sol: 63.74 %
• Crystal grow: Temperature: 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

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
• Detector: Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2006
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.1159 Å / Relative weight: 1
• Reflection: Resolution: 1.86→42.341 Å / Num. obs: 33284 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / R_merge(I) obs: 0.129 / Net I/σ(I): 5.8
• Reflection shell: Resolution: 1.86→1.98 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 96.4

Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
Coot		model building
CNS		phasing
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Resolution: 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

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.1684	1910	5.85 %	random
Rwork	0.1396	-	-	-
obs	0.1413	33284	99.91 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.86→42.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1994	0	67	282	2343

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2131
X-RAY DIFFRACTION	f_angle_d	1.316	2908
X-RAY DIFFRACTION	f_dihedral_angle_d	12.705	797
X-RAY DIFFRACTION	f_chiral_restr	0.057	330
X-RAY DIFFRACTION	f_plane_restr	0.007	394

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.86-1.8845	0.2341	144	0.2265	2313	X-RAY DIFFRACTION	100
1.8845-1.9103	0.2166	139	0.1989	2277	X-RAY DIFFRACTION	100
1.9103-1.9376	0.2323	148	0.1809	2282	X-RAY DIFFRACTION	100
1.9376-1.9665	0.185	148	0.1694	2292	X-RAY DIFFRACTION	100
1.9665-1.9972	0.174	144	0.1617	2326	X-RAY DIFFRACTION	100
1.9972-2.03	0.2196	137	0.1595	2265	X-RAY DIFFRACTION	100
2.03-2.065	0.1903	147	0.1562	2292	X-RAY DIFFRACTION	100
2.065-2.1025	0.1667	141	0.1503	2293	X-RAY DIFFRACTION	100
2.1025-2.143	0.1622	140	0.1474	2303	X-RAY DIFFRACTION	100
2.143-2.1867	0.1564	144	0.1457	2289	X-RAY DIFFRACTION	100
2.1867-2.2343	0.1782	143	0.1377	2318	X-RAY DIFFRACTION	100
2.2343-2.2862	0.1497	135	0.129	2308	X-RAY DIFFRACTION	100
2.2862-2.3434	0.1573	145	0.1273	2273	X-RAY DIFFRACTION	100
2.3434-2.4067	0.1843	138	0.1257	2281	X-RAY DIFFRACTION	100
2.4067-2.4776	0.1889	146	0.1289	2298	X-RAY DIFFRACTION	100
2.4776-2.5575	0.1861	143	0.1406	2308	X-RAY DIFFRACTION	100
2.5575-2.6489	0.1954	139	0.1344	2312	X-RAY DIFFRACTION	100
2.6489-2.755	0.1789	140	0.1309	2291	X-RAY DIFFRACTION	100
2.755-2.8803	0.1697	145	0.1343	2303	X-RAY DIFFRACTION	100
2.8803-3.0321	0.1682	139	0.134	2292	X-RAY DIFFRACTION	100
3.0321-3.222	0.1753	148	0.141	2285	X-RAY DIFFRACTION	100
3.222-3.4707	0.173	142	0.1423	2293	X-RAY DIFFRACTION	100
3.4707-3.8198	0.1608	146	0.1343	2304	X-RAY DIFFRACTION	100
3.8198-4.372	0.1455	143	0.1273	2294	X-RAY DIFFRACTION	100
4.372-5.5064	0.1417	145	0.1239	2304	X-RAY DIFFRACTION	100
5.5064-42.3518	0.15	138	0.1477	2273	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Origin x: 45.5974 Å / Origin y: 48.1684 Å / Origin z: 52.5347 Å

	11	12	13	21	22	23	31	32	33
T	0.1277 Å2	-0.0043 Å2	-0.0111 Å2	-	0.2186 Å2	0.0109 Å2	-	-	0.1636 Å2
L	0.245 °2	-0.0682 °2	0.1397 °2	-	0.2795 °2	0.0045 °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 group: Selection details: all