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- PDB-5i7s: Crystal structure of B. pseudomallei FabI in complex with NAD and PT01 -

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Basic information

Entry
Database: PDB / ID: 5i7s
TitleCrystal structure of B. pseudomallei FabI in complex with NAD and PT01
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-2-PHENOXYPHENOL / 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: 1.595 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 18, 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: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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
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)30,2033
Polymers29,3251
Non-polymers8782
Water6,107339
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)120,81212
Polymers117,3024
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18980 Å2
ΔGint-142 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.430, 75.860, 89.110
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-454-

HOH

21A-548-

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-E9P / 5-ETHYL-2-PHENOXYPHENOL


Mass: 214.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.595→31.284 Å / Num. obs: 33816 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.2
Reflection shellResolution: 1.595→1.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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Processing

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

3ek2


Resolution: 1.595→31.284 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.95
RfactorNum. reflection% reflection
Rfree0.1784 1708 5.05 %
Rwork0.1521 --
obs0.1534 33812 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.595→31.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 60 339 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072021
X-RAY DIFFRACTIONf_angle_d1.1452745
X-RAY DIFFRACTIONf_dihedral_angle_d13.58719
X-RAY DIFFRACTIONf_chiral_restr0.076315
X-RAY DIFFRACTIONf_plane_restr0.005349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.595-1.64190.24331280.23082631X-RAY DIFFRACTION99
1.6419-1.69490.23651300.20652648X-RAY DIFFRACTION99
1.6949-1.75550.22991270.1912651X-RAY DIFFRACTION100
1.7555-1.82580.19641600.17122642X-RAY DIFFRACTION99
1.8258-1.90890.19571360.15722631X-RAY DIFFRACTION99
1.9089-2.00950.17751410.14752649X-RAY DIFFRACTION100
2.0095-2.13540.1641370.13782661X-RAY DIFFRACTION100
2.1354-2.30020.15061580.13392665X-RAY DIFFRACTION100
2.3002-2.53160.19151620.14172662X-RAY DIFFRACTION100
2.5316-2.89770.17651420.14812705X-RAY DIFFRACTION100
2.8977-3.64990.15641410.13742732X-RAY DIFFRACTION100
3.6499-31.29040.16981460.14732827X-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)
11.2958-0.1039-0.38190.4963-0.14420.66330.15760.1028-0.2758-0.082-0.00230.07040.1417-0.38650.03020.0672-0.0615-0.04140.13910.03720.084810.3377-5.1205-19.5579
21.5798-0.33560.3820.587-0.3630.8878-0.03160.08570.0248-0.10940.0517-0.00690.0114-0.141-0.01290.0678-0.0102-0.00440.06870.03020.030418.52191.5041-24.0336
30.5429-0.18680.01520.4925-0.07190.57930.00620.0213-0.0378-0.03260.0350.02950.0229-0.0249-0.03620.0359-0.0134-0.00620.01730.00450.034130.606-0.9952-16.7819
40.7557-0.21460.19221.5623-0.15280.66870.06890.1408-0.1069-0.161-0.02840.02070.09-0.0532-0.04160.05890.0056-0.0130.04050.02040.038523.7386-6.0826-12.1211
50.70780.02210.18320.4873-0.13630.71880.03520.1159-0.18750.01860.07880.06670.1201-0.0993-0.04210.0521-0.0228-0.0180.02840.01440.04123.1333-9.5383-2.6195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 202 )
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 258 )

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