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- PDB-4cl6: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -

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Basic information

Entry
Database: PDB / ID: 4cl6
TitleCrystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with N-(4- Chlorobenzyl)-3-(2-furyl)-1H-1,2,4-triazol-5-amine
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 / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / 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
Chem-7SB / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsMoynie, L. / McMahon, S.A. / Duthie, F.G. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A Substrate Mimic Allows High Throughput Assay of the Faba Protein and Consequently the Identification of a Novel Inhibitor of Pseudomonas Aeruginosa Faba.
Authors: Moynie, L. / Hope, A.G. / Finzel, K. / Schmidberger, J. / Leckie, S.M. / Schneider, G. / Burkart, M.D. / Smith, A.D. / Gray, D.W. / Naismith, J.H.
History
DepositionJan 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Mar 2, 2016Group: Database references
Revision 1.4Jun 13, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)95,21610
Polymers93,8435
Non-polymers1,3745
Water4,882271
1
A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0864
Polymers37,5372
Non-polymers5492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-16.3 kcal/mol
Surface area13280 Å2
MethodPISA
2
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)38,0864
Polymers37,5372
Non-polymers5492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3830 Å2
ΔGint-17.8 kcal/mol
Surface area13480 Å2
MethodPISA
3
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0864
Polymers37,5372
Non-polymers5492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-16.1 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.610, 142.870, 77.850
Angle α, β, γ (deg.)90.00, 116.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2013-

HOH

21E-2034-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA2 - 1712 - 171
21PHEPHEBB2 - 1712 - 171
12PHEPHEAA2 - 1712 - 171
22PHEPHECC2 - 1712 - 171
13PHEPHEAA2 - 1712 - 171
23PHEPHEDD2 - 1712 - 171
14PHEPHEAA2 - 1712 - 171
24PHEPHEEE2 - 1712 - 171
15SERSERBB2 - 1702 - 170
25SERSERCC2 - 1702 - 170
16PHEPHEBB2 - 1712 - 171
26PHEPHEDD2 - 1712 - 171
17PHEPHEBB2 - 1712 - 171
27PHEPHEEE2 - 1712 - 171
18SERSERCC2 - 1702 - 170
28SERSERDD2 - 1702 - 170
19SERSERCC2 - 1702 - 170
29SERSEREE2 - 1702 - 170
110PHEPHEDD2 - 1712 - 171
210PHEPHEEE2 - 1712 - 171

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(0.3053, 0.5926, 0.7454), (0.5977, -0.7286, 0.3345), (0.7413, 0.3434, -0.5766)-75.5329, 121.7074, 35.0225
2given(0.4733, -0.3722, 0.7984), (-0.367, -0.9073, -0.2054), (0.8008, -0.1958, -0.566)-2.8314, 136.9412, 68.6489
3given(0.5269, -0.799, -0.2898), (0.814, 0.3763, 0.4426), (-0.2446, -0.4691, 0.8486)56.0662, 42.6952, 39.5398
4given(0.5116, 0.8134, -0.2769), (-0.8179, 0.3623, -0.4469), (-0.2632, 0.4551, 0.8507)-54.1186, 46.6124, -35.9553

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Components

#1: Protein
3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE / 3-HYDROXYDECANOYL-ACYL-CARRIER-PROTEIN DEHYDRATASE / 3-HYDROXYACYL-[ACYL-CARRIER-PROTEIN] ...3-HYDROXYDECANOYL-ACYL-CARRIER-PROTEIN DEHYDRATASE / 3-HYDROXYACYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE FABA / BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE / TRANS-2-DECENOYL-[ACYL-CARRIER-PROTEIN] ISOMERASE


Mass: 18768.533 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER
References: UniProt: O33877, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, trans-2-decenoyl-[acyl-carrier protein] isomerase, EC: 4.2.1.60
#2: Chemical
ChemComp-7SB / N-(4-chlorobenzyl)-5-(furan-2-yl)-1H-1,2,4-triazol-3-amine


Mass: 274.706 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H11ClN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 3.06 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5
Details: 0.1 M LITHIUM SULPHATE, 12 % PEG MME 5000, 0.1 M SODIUM CITRATE PH 5

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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: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.41→43.51 Å / Num. obs: 42735 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B0C

4b0c


Resolution: 2.41→43.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.064 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21169 2153 5 %RANDOM
Rwork0.18201 ---
obs0.18355 40582 97.38 %-
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: 43.357 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.42 Å2
2---0.05 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.41→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6551 0 95 271 6917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196810
X-RAY DIFFRACTIONr_bond_other_d0.0050.026452
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9759210
X-RAY DIFFRACTIONr_angle_other_deg0.93.00214792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0975843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1223.211299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.421151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6131549
X-RAY DIFFRACTIONr_chiral_restr0.080.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217796
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021654
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100290.06
12B100290.06
21A99530.06
22C99530.06
31A99750.06
32D99750.06
41A99830.05
42E99830.05
51B99500.06
52C99500.06
61B100640.07
62D100640.07
71B100270.06
72E100270.06
81C99570.06
82D99570.06
91C98820.07
92E98820.07
101D99500.07
102E99500.07
LS refinement shellResolution: 2.405→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 142 -
Rwork0.279 2914 -
obs--94.88 %
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)
17.2605-5.83420.044723.5992-5.65881.6947-0.4178-0.3689-1.51591.6330.32031.0966-0.314-0.15030.09750.3864-0.42130.37580.9203-0.31360.6858-53.88444.64330.631
21.1875-0.5919-0.97252.59930.45932.89460.0602-0.0636-0.20790.2018-0.18770.32550.1196-0.22090.12760.041-0.03650.00860.2302-0.02950.102-45.56951.19921.754
34.3781-2.2154-0.75957.07310.90274.98240.1693-0.46840.39360.4847-0.0340.029-0.2928-0.0776-0.13530.0839-0.05540.03380.24110.02750.0801-40.59556.04727.156
42.405-2.75852.530615.7386.41959.7390.15260.21170.1989-1.7211-0.5294-0.1184-1.0933-0.38670.37680.30290.2302-0.0910.9445-0.14330.0957-42.92465.181-7.28
53.374-0.8856-1.64352.0986-0.05033.5240.18920.288-0.0526-0.3352-0.31170.0984-0.1487-0.16960.12250.06330.068-0.02680.1791-0.0050.0396-42.77664.8897.018
65.8098-1.0795-1.31398.72461.18074.58670.3266-0.12990.1539-0.4675-0.1139-0.7985-0.03210.5759-0.21270.06630.05450.04850.22510.03310.0876-34.43565.9818.609
74.47262.4186-1.19486.7871-1.91412.8153-0.12980.1650.1372-0.2379-0.104-0.50530.08390.41380.23380.19080.00280.03210.29870.06790.1449-21.591105.5662.381
82.56920.7346-1.85873.3030.02932.91380.1068-0.22980.12650.2095-0.2456-0.2288-0.31060.32510.13870.172-0.0219-0.02180.26130.04890.1641-27.199102.63713.798
94.43490.26360.41216.40992.23278.85050.2010.2637-0.47120.1087-0.2028-0.75521.17210.32440.00190.2417-0.02540.03120.34170.16440.3093-22.04693.028.481
104.87182.40371.146219.986610.05555.1240.5666-0.2428-0.11071.0737-1.08081.11210.4207-0.66590.51420.31560.08650.17160.5283-0.12040.2337-53.51694.83125.858
111.65951.0074-0.64872.6859-0.15883.32710.0597-0.18860.13370.1159-0.12780.0282-0.1625-0.06410.0680.07640.02670.00080.17480.00280.1069-41.88692.31117.769
123.35641.95031.15258.14772.55987.87380.3335-0.53080.03040.8112-0.0789-0.57640.25540.5251-0.25450.10590.0051-0.00930.27860.02730.1536-37.17188.05323.428
133.20010.0989-0.99931.94790.21724.8660.067-0.2648-0.02090.16560.00230.11770.4016-0.0945-0.06930.0949-0.0123-0.02790.06350.01450.0347-15.54536.94146.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION2A15 - 121
3X-RAY DIFFRACTION3A122 - 171
4X-RAY DIFFRACTION4B2 - 19
5X-RAY DIFFRACTION5B20 - 121
6X-RAY DIFFRACTION6B122 - 171
7X-RAY DIFFRACTION7C1 - 53
8X-RAY DIFFRACTION8C54 - 131
9X-RAY DIFFRACTION9C132 - 171
10X-RAY DIFFRACTION10D1 - 19
11X-RAY DIFFRACTION11D20 - 121
12X-RAY DIFFRACTION12D122 - 171
13X-RAY DIFFRACTION13E2 - 171

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