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- PDB-4b8u: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -

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Basic information

Entry
Database: PDB / ID: 4b8u
TitleCrystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with N- isobutyl-2-(5-(2-thienyl)-1,2-oxazol-3-yl-)methoxy)acetamide
Components3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
KeywordsLYASE / FATTY ACID BIOSYNTHESIS / INHIBITOR / BACTERIAL VIRULENCE / DRUG DISCOVERY
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-IBK / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsMoynie, L. / McMahon, S.A. / Duthie, F.G. / Brenk, R. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Insights Into the Mechanism and Inhibition of the Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase from Pseudomonasaeruginosa.
Authors: Moynie, L. / Leckie, S.M. / Mcmahon, S.A. / Duthie, F.G. / Koehnke, A. / Taylor, J.W. / Alphey, M.S. / Brenk, R. / Smith, A.D. / Naismith, J.H.
History
DepositionAug 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Other
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Dec 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2337
Polymers93,8435
Non-polymers3902
Water45025
1
A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8313
Polymers37,5372
Non-polymers2941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-17.7 kcal/mol
Surface area13600 Å2
MethodPISA
2
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6333
Polymers37,5372
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-29.9 kcal/mol
Surface area13440 Å2
MethodPISA
3
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE


Theoretical massNumber of molelcules
Total (without water)37,5372
Polymers37,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3200 Å2
ΔGint-17.9 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.900, 143.670, 78.000
Angle α, β, γ (deg.)90.00, 116.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE / BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE


Mass: 18768.533 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: O33877, EC: 4.2.1.60
#2: Chemical ChemComp-IBK / N-isobutyl-2-{[5-(thiophen-2-yl)-1,2-oxazol-3-yl]methoxy}acetamide


Mass: 294.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2O3S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.05 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5
Details: PEG MME 5000 13 %, 100 MM SODIUM CITRATE PH 5.0, LITHIUM SULPHATE 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.78→71.83 Å / Num. obs: 27828 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5
Reflection shellResolution: 2.76→2.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FQ9

4fq9


Resolution: 2.76→71.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 25.72 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 1.866 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22451 1399 5 %RANDOM
Rwork0.18274 ---
obs0.18483 26426 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.37 Å2
2--1.39 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.76→71.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 25 25 6481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196606
X-RAY DIFFRACTIONr_bond_other_d0.0050.024535
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9638932
X-RAY DIFFRACTIONr_angle_other_deg1.1343.00110979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8685826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94223.299294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.198151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8241547
X-RAY DIFFRACTIONr_chiral_restr0.0850.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217429
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021429
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.762→2.834 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 100 -
Rwork0.331 1935 -
obs--98.55 %
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)
13.4542-0.9289-0.59323.95510.79123.10890.54630.60860.0081-1.0246-0.7351-0.07980.08920.10160.18880.47050.3905-0.02340.45020.09450.183-39.582765.60276.0631
22.9656-1.2591-0.56814.02530.09853.35760.31140.0861-0.16930.0753-0.4430.5756-0.0572-0.31780.13160.0923-0.0223-0.00850.2628-0.08790.2732-44.532552.326523.5894
30.7548-0.5684-0.73924.48910.46323.75170.09970.17240.0886-0.3852-0.3870.127-0.1661-0.3030.28730.2214-0.06860.0060.3121-0.10380.3512-15.428819.8132-19.6585
42.1491-1.1196-1.27014.02891.5883.61790.08050.2059-0.125-0.1024-0.56260.6397-0.1346-0.85690.48210.28370.0358-0.08970.6259-0.29270.529-33.261430.1891-9.4125
52.6561-0.2947-1.14072.1626-0.30734.55450.11740.216-0.1298-0.0891-0.1205-0.11770.7070.02740.00310.23640.0272-0.03780.032-0.03440.136-19.139636.972323.7666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 171
2X-RAY DIFFRACTION2B3 - 171
3X-RAY DIFFRACTION3C2 - 166
4X-RAY DIFFRACTION4D3 - 169
5X-RAY DIFFRACTION5E3 - 171

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