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- PDB-5i9l: Crystal structure of B. pseudomallei FabI in complex with NAD and... -

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Basic information

Entry
Database: PDB / ID: 5i9l
TitleCrystal structure of B. pseudomallei FabI in complex with NAD and PT404
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
Chem-9W7 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)30,3934
Polymers29,3251
Non-polymers1,0673
Water2,756153
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)121,57016
Polymers117,3024
Non-polymers4,26912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area19910 Å2
ΔGint-142 kcal/mol
Surface area30120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.579, 75.063, 86.375
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-447-

HOH

21A-465-

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-9W7 / 2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol


Mass: 311.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11ClFNO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.99 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bistris, pH 6.5, 30 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→43.19 Å / Num. obs: 22817 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.531 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.2138 1082 5.09 %
Rwork0.175 --
obs0.1769 21245 93.04 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 41.525 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.0275 Å20 Å20 Å2
2--4.0123 Å20 Å2
3---8.0152 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 71 153 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062024
X-RAY DIFFRACTIONf_angle_d1.1472747
X-RAY DIFFRACTIONf_dihedral_angle_d14.186731
X-RAY DIFFRACTIONf_chiral_restr0.074313
X-RAY DIFFRACTIONf_plane_restr0.004348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8820.30031280.23392231X-RAY DIFFRACTION84
1.882-1.98120.23941310.20232313X-RAY DIFFRACTION87
1.9812-2.10540.23521290.19422362X-RAY DIFFRACTION89
2.1054-2.26790.23021400.182513X-RAY DIFFRACTION93
2.2679-2.49610.22141180.18722581X-RAY DIFFRACTION95
2.4961-2.85720.21581380.18592643X-RAY DIFFRACTION97
2.8572-3.59930.21281670.17272671X-RAY DIFFRACTION99
3.5993-37.53960.18861310.1562849X-RAY DIFFRACTION100
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)
10.20210.1632-0.31630.52230.20781.26960.065-0.28020.2547-0.03650.2013-0.09530.02050.8589-0.00860.2328-0.08290.04810.5824-0.26560.323726.76721.6715-14.4306
20.15360.11210.05660.44180.04490.61470.2917-0.20930.3853-0.16680.2505-0.2747-0.1990.60410.16010.1996-0.16410.0770.569-0.23020.34526.57386.026-16.2936
30.0020.0036-0.00320.0005-0.00960.0185-0.0222-0.02060.0380.0077-0.04210.07-0.03440.0797-0.03830.3211-0.38020.27080.7346-0.17640.786525.888611.9331-29.4587
40.6512-0.0439-0.09770.3626-0.34510.8220.1660.13980.1395-0.16720.11810.0071-0.13940.6649-0.01080.2373-0.04660.05460.495-0.16430.248624.3365-0.7448-24.2495
50.8741-0.1641-0.2480.2857-0.0011.0378-0.01790.39750.3521-0.0360.2335-0.0299-0.10530.21250.03270.196-0.01910.03560.2047-0.06980.25126.14982.628-22.2168
60.37040.1695-0.04680.5459-0.29990.98370.10550.06610.14830.04890.11890.0873-0.090.16980.11630.1881-0.01340.02880.1761-0.06660.25288.77011.5604-11.3802
70.0692-0.0810.07760.1588-0.09040.0838-0.04960.40790.1389-0.0585-0.0481-0.0104-0.16230.0261-0.01880.4849-0.02360.12680.38980.07440.55628.453820.1681-14.1595
80.25090.13460.3290.4734-0.02891.04590.00070.10750.01120.06210.2062-0.0073-0.18050.37150.12510.2187-0.05530.04350.2427-0.09970.271514.23358.7317-1.6762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:17)
2X-RAY DIFFRACTION2(chain A and resid 18:42)
3X-RAY DIFFRACTION3(chain A and resid 43:48)
4X-RAY DIFFRACTION4(chain A and resid 49:93)
5X-RAY DIFFRACTION5(chain A and resid 94:138)
6X-RAY DIFFRACTION6(chain A and resid 139:194)
7X-RAY DIFFRACTION7(chain A and resid 195:206)
8X-RAY DIFFRACTION8(chain A and resid 207:258)

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