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- PDB-4bku: Enoyl-ACP reductase FabI from Burkholderia pseudomallei with cofa... -

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Basic information

Entry
Database: PDB / ID: 4bku
TitleEnoyl-ACP reductase FabI from Burkholderia pseudomallei with cofactor NADH and inhibitor PT155
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS / ENOYL- ACP REDUCTASE / PYRIDONE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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-1S5 / 1,4-DIHYDRONICOTINAMIDE 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: 1.841 Å
AuthorsHirschbeck, M.W. / Liu, N. / Neckles, C. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor.
Authors: Schiebel, J. / Chang, A. / Shah, S. / Lu, Y. / Liu, L. / Pan, P. / Hirschbeck, M.W. / Tareilus, M. / Eltschkner, S. / Yu, W. / Cummings, J.E. / Knudson, S.E. / Bommineni, G.R. / Walker, S.G. ...Authors: Schiebel, J. / Chang, A. / Shah, S. / Lu, Y. / Liu, L. / Pan, P. / Hirschbeck, M.W. / Tareilus, M. / Eltschkner, S. / Yu, W. / Cummings, J.E. / Knudson, S.E. / Bommineni, G.R. / Walker, S.G. / Slayden, R.A. / Sotriffer, C.A. / Tonge, P.J. / Kisker, C.
History
DepositionApr 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Atomic model / Database references
Revision 1.3Dec 10, 2014Group: Data collection
Revision 1.4Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)30,3053
Polymers29,3251
Non-polymers9802
Water6,179343
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)121,22112
Polymers117,3024
Non-polymers3,9198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area18940 Å2
ΔGint-119.4 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.320, 75.950, 89.420
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-2006-

HOH

21A-2258-

HOH

31A-2327-

HOH

41A-2335-

HOH

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Components

#1: Protein ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / ENOYL-ACP REDUCTASE FABI


Mass: 29325.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: BP82 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I1WHT9, UniProt: A0A0H3HP34*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-1S5 / 5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium


Mass: 314.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNCBI REFERENCE SEQUENCE YP_108799.1

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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: 2.15 Å3/Da / Density % sol: 42.83 % / Description: NONE
Crystal growDetails: 20% PEG 3350 200 MM (NH4)2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→37.97 Å / Num. obs: 22291 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EK2

3ek2


Resolution: 1.841→28.578 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 13.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1621 1140 5.1 %
Rwork0.137 --
obs0.1383 22268 99.87 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.834 Å2 / ksol: 0.436 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3323 Å20 Å20 Å2
2--0.1615 Å20 Å2
3---2.1708 Å2
Refinement stepCycle: LAST / Resolution: 1.841→28.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 67 343 2322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082073
X-RAY DIFFRACTIONf_angle_d1.1372828
X-RAY DIFFRACTIONf_dihedral_angle_d14.386762
X-RAY DIFFRACTIONf_chiral_restr0.077325
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.841-1.92480.22431470.19132599X-RAY DIFFRACTION100
1.9248-2.02620.20311530.13852585X-RAY DIFFRACTION100
2.0262-2.15310.1611420.13032623X-RAY DIFFRACTION100
2.1531-2.31930.14791350.12232629X-RAY DIFFRACTION100
2.3193-2.55260.16811360.132633X-RAY DIFFRACTION100
2.5526-2.92160.16281390.13572636X-RAY DIFFRACTION100
2.9216-3.67970.15151590.13212659X-RAY DIFFRACTION100
3.6797-28.58140.14171290.14042764X-RAY DIFFRACTION99
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)
10.9870.4241-0.18841.6262-0.62951.7548-0.01190.0394-0.0517-0.06010.0313-0.06330.09850.149-0.02580.06320.0394-0.01280.119-0.02090.0759-10.1995-3.806915.0096
25.7842.7933-4.24784.6189-3.56717.85080.111-0.3317-0.19890.26020.12760.02950.3212-0.0175-0.21180.12840.0242-0.06480.11310.03570.1395-9.165-10.895125.8298
30.89830.21280.13680.3103-0.010.4459-0.0062-0.035-0.03820.03250.0031-0.0242-0.00070.0270.00180.0660.0148-0.00040.0604-0.00730.0664-25.583-0.367919.7677
40.55430.5481-0.1643.0841-1.06421.0161-0.0106-0.0432-0.0464-0.01450.04760.12220.12490.0329-0.03870.06520.01080.00820.0802-0.00640.0741-23.8563-8.352712.3702
51.17230.23720.28591.57710.51211.0745-0.00330.0165-0.13210.02540.0197-0.02050.10780.0523-0.01310.06090.01560.01510.05520.00310.0302-22.8453-9.20672.2762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:41)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 42:55)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 56:178)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 179:203)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 204:256)

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