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- PDB-5i8w: Crystal structure of B. pseudomallei FabI in complex with NAD and... -

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Basic information

Entry
Database: PDB / ID: 5i8w
TitleCrystal structure of B. pseudomallei FabI in complex with NAD and PT401
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
4-fluoro-5-hexyl-2-(2-methylphenoxy)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: 1.629 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 19, 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)30,2913
Polymers29,3251
Non-polymers9662
Water4,720262
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)121,16512
Polymers117,3024
Non-polymers3,8638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area19030 Å2
ΔGint-140 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.700, 75.690, 88.360
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-476-

HOH

21A-480-

HOH

31A-508-

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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-69H / 4-fluoro-5-hexyl-2-(2-methylphenoxy)phenol


Mass: 302.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23FO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bistris, pH 6.5, 36 % 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 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.629→28.74 Å / Num. obs: 29346 / % possible obs: 93 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.9
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 8.7 / % possible all: 88.4

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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: 1.629→26.584 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.51
RfactorNum. reflection% reflection
Rfree0.1924 1493 5.09 %
Rwork0.1626 --
obs0.1641 29337 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.629→26.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 66 262 2240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062016
X-RAY DIFFRACTIONf_angle_d1.1732734
X-RAY DIFFRACTIONf_dihedral_angle_d13.917716
X-RAY DIFFRACTIONf_chiral_restr0.077312
X-RAY DIFFRACTIONf_plane_restr0.004346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.629-1.68160.2441110.18892381X-RAY DIFFRACTION87
1.6816-1.74170.19461480.18132383X-RAY DIFFRACTION90
1.7417-1.81140.23551260.17732467X-RAY DIFFRACTION91
1.8114-1.89380.23091270.17522449X-RAY DIFFRACTION91
1.8938-1.99360.21391460.16442491X-RAY DIFFRACTION92
1.9936-2.11850.17021320.17042494X-RAY DIFFRACTION92
2.1185-2.28190.1871500.15662542X-RAY DIFFRACTION94
2.2819-2.51140.18091290.16552583X-RAY DIFFRACTION94
2.5114-2.87450.20141320.16372645X-RAY DIFFRACTION95
2.8745-3.62010.19311620.15652645X-RAY DIFFRACTION96
3.6201-26.58720.17621300.15622764X-RAY DIFFRACTION96
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)
12.00660.4899-1.0561.2420.20183.26240.1833-0.1846-0.34450.00780.10640.0060.2397-0.7154-0.16240.1777-0.1089-0.07330.41250.14230.2062-26.8816-3.986729.2934
25.70371.209-1.1052.5765-0.81920.37010.30370.0141-0.9365-0.1768-0.02630.02520.5373-0.4818-0.07930.2747-0.1615-0.13730.44280.0390.3-27.0252-7.0818.2217
33.3546-1.31650.64621.0956-0.05453.41820.07170.05650.0095-0.21230.14460.1499-0.0637-0.505-0.2080.1503-0.036-0.01120.21930.08060.1596-21.34723.946920.2149
42.3218-0.8084-0.03280.5314-0.54261.69520.03120.1002-0.1221-0.07560.0521-0.00450.1047-0.1071-0.07350.1369-0.0408-0.02550.0986-0.00570.1632-6.4543-3.225.5103
51.8831-0.3404-0.35450.1508-0.16892.19270.04730.1266-0.2502-0.04860.01490.07180.1448-0.1694-0.03020.1021-0.0298-0.02830.10340.01710.145-9.7939-2.027631.4214
62.175-1.03830.5493.9142-0.94992.12110.01820.1461-0.2559-0.12060.1380.21660.2919-0.3212-0.16240.1488-0.0716-0.01450.20580.03960.0929-16.1198-10.14140.9435
72.94592.827-0.25774.1005-1.60436.60260.05360.0298-0.3131-0.09620.10070.13280.3126-0.0343-0.18080.101-0.0265-0.00730.085-0.00070.0913-8.4671-8.789243.9618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 202 )
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 242 )
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 258 )

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