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- PDB-4b0b: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -

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Basic information

Entry
Database: PDB / ID: 4b0b
TitleCrystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with 3-(pyridin-2-yloxy)aniline
Components3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
KeywordsLYASE / FATTY ACID BIOSYNTHESIS / 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 / : / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / 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
3-(pyridin-2-yloxy)aniline / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoynie, L. / McMahon, S.A. / Duthie, F.G. / Taylor, J.W. / 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
DepositionJul 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9094
Polymers37,5372
Non-polymers3722
Water5,386299
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-16.6 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.320, 117.990, 47.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A2 - 107
2112B2 - 107
1212A112 - 151
2212B112 - 151
1312A152 - 171
2312B152 - 171

NCS oper: (Code: given
Matrix: (-0.9995, -0.03104, 0.002804), (-0.03096, 0.9992, 0.02352), (-0.003532, 0.02343, -0.9997)
Vector: 25.89, 0.1637, 23.46)

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Components

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


Mass: 18768.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / 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-54F / 3-(pyridin-2-yloxy)aniline


Mass: 186.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.3 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growpH: 8
Details: 15 % PEG 8000,0.2 M MAGNESIUM CHLORIDE, TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX / Wavelength: 1.54178
DetectorType: RIGAKU CCD / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→37.3 Å / Num. obs: 26978 / % possible obs: 99 % / Observed criterion σ(I): -3.7 / Redundancy: 7.78 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.43 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.21 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FQ9

4fq9


Resolution: 1.9→37.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.29 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1353 5 %RANDOM
Rwork0.20318 ---
obs0.20486 25582 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.83 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 28 299 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222742
X-RAY DIFFRACTIONr_bond_other_d00.021894
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.973712
X-RAY DIFFRACTIONr_angle_other_deg0.7473.0044574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0125345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57723.171123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7331521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
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_it1.511.51685
X-RAY DIFFRACTIONr_mcbond_other0.5841.5710
X-RAY DIFFRACTIONr_mcangle_it2.2522695
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.70331057
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6324.51015
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A964tight positional0.080.05
2B964tight positional0.080.05
1A1215medium positional0.340.5
2B1215medium positional0.340.5
1A964tight thermal10.5
2B964tight thermal10.5
1A1215medium thermal1.362
2B1215medium thermal1.362
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 92 -
Rwork0.358 1822 -
obs--100 %
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)
12.0368-1.69870.4753.3953-1.64886.92360.01570.2682-0.1275-0.1429-0.117-0.32580.34170.59390.10130.13090.07910.06150.1324-0.02450.196428.1189.315-3.342
21.1849-0.0131-0.09680.5005-0.06431.22780.04330.03410.0176-0.0204-0.0365-0.05770.02680.0894-0.00680.08080.00290.01350.0108-0.00560.101417.78717.7762.602
30.8890.24970.19611.07750.85322.7070.1289-0.31860.04010.0080.0461-0.2007-0.05750.1249-0.1750.1227-0.0440.01720.1419-0.01730.171320.75822.3719.21
41.60940.82161.57094.84371.73875.7166-0.0916-0.2128-0.06560.361-0.11840.62630.4388-0.40180.210.1558-0.04310.09380.08560.02730.1891-2.4038.48427.059
51.27-0.1685-0.65470.63090.08271.56640.0071-0.1586-0.04580.0785-0.00160.056-0.023-0.0012-0.00550.08520.00320.00250.03520.010.08487.66317.39621.271
64.5388-0.37211.38811.5351-0.4073.0720.05910.20770.1246-0.06490.02530.1127-0.09250.0103-0.08440.15660.0040.05430.1023-0.0140.14844.51622.10114.679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 19
2X-RAY DIFFRACTION2A20 - 151
3X-RAY DIFFRACTION3A152 - 171
4X-RAY DIFFRACTION4B2 - 19
5X-RAY DIFFRACTION5B20 - 151
6X-RAY DIFFRACTION6B152 - 171

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