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- PDB-5i9n: Crystal structure of B. pseudomallei FabI in complex with NAD and... -

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Basic information

Entry
Database: PDB / ID: 5i9n
TitleCrystal structure of B. pseudomallei FabI in complex with NAD and PT412
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-ACP reductase / Burkholderia pseudomallei / diphenyl ethers / slow-binding inhibitors
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
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
5-ethyl-4-fluoro-2-(2-nitrophenoxy)phenol / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.512 Å
AuthorsHirschbeck, M.W. / Eltschkner, S. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: Biochemistry / Year: 2017
Title: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
Authors: Neckles, C. / Eltschkner, S. / Cummings, J.E. / Hirschbeck, M. / Daryaee, F. / Bommineni, G.R. / Zhang, Z. / Spagnuolo, L. / Yu, W. / Davoodi, S. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)30,2663
Polymers29,3251
Non-polymers9412
Water2,018112
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)121,06412
Polymers117,3024
Non-polymers3,7638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area19140 Å2
ΔGint-137 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.630, 74.670, 96.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-479-

HOH

31A-495-

HOH

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Components

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


Mass: 29325.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: fabI, fabI_2, ACT79_25590, AM256_11615, AM257_11635, AMS56_08605, DP46_2957, DP49_6839, ERS012314_03793, ERS012372_03823, SY87_14645, TR70_1075, VU09_13745
Production host: Escherichia coli (E. coli)
References: UniProt: A0A069B9A4, UniProt: A0A0H3HP34*PLUS, 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-69J / 5-ethyl-4-fluoro-2-(2-nitrophenoxy)phenol


Mass: 277.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12FNO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.16 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bistris, pH 6.5, 30 % PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.51→59.11 Å / Num. obs: 8929 / % possible obs: 96.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 2.51→2.65 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 6.4 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK2

3ek2


Resolution: 2.512→29.607 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 457 5.13 %
Rwork0.1561 --
obs0.1591 8906 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.512→29.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 64 112 2114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072039
X-RAY DIFFRACTIONf_angle_d1.092768
X-RAY DIFFRACTIONf_dihedral_angle_d13.632721
X-RAY DIFFRACTIONf_chiral_restr0.069316
X-RAY DIFFRACTIONf_plane_restr0.004352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.512-2.87530.24721400.1692731X-RAY DIFFRACTION94
2.8753-3.62150.21871490.15852789X-RAY DIFFRACTION96
3.6215-29.60860.20091680.14912929X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80580.40350.57822.0715-0.8252.63120.09860.06130.00550.09890.01670.1587-0.69910.3327-0.13320.6038-0.09640.14140.1748-0.07730.27843.0256-10.957614.6233
20.7902-0.0383-0.28771.8259-1.16141.82870.2594-0.08340.2330.16390.1802-0.2892-0.66290.12540.16550.715-0.17840.13570.2704-0.04510.26044.5596-9.894515.3277
31.39840.64060.62834.43471.36250.95780.0809-0.3668-0.25950.5791-0.0201-0.3444-0.15110.0903-0.07231.2249-0.5835-0.12530.4683-0.21590.440610.7901-9.338626.9313
40.7178-0.3277-0.4972.72920.7291.43050.014-0.17830.08640.65410.1185-0.0116-0.55240.2519-0.16730.5341-0.01720.07690.2446-0.00650.20921.7681-21.360924.1447
51.1944-0.0943-0.09621.91240.02591.91490.19160.04180.00080.255-0.0261-0.0114-0.2378-0.0521-0.19480.1939-0.01090.03560.1807-0.00290.1901-0.3998-29.35216.434
62.76470.81320.12371.6675-0.20472.29550.0549-0.124-0.01460.34130.1614-0.0844-0.48250.4771-0.1510.2126-0.0660.0510.242-0.05750.21236.3257-23.748112.0718
70.88460.1257-0.1741.4411-0.47411.6770.1259-0.11820.09370.11790.0708-0.2062-0.4420.4149-0.15780.227-0.08080.02370.3069-0.05520.23219.4649-23.19262.5233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 109 )
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 178 )
6X-RAY DIFFRACTION6chain 'A' and (resid 179 through 202 )
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 258 )

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