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- PDB-7bis: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehyd... -

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Basic information

Entry
Database: PDB / ID: 7bis
TitleCrystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA)from Pseudomonas aeruginosa in complex with DDD00082063
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / FabA / PA1610
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 / (3R)-hydroxyacyl-[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 domain superfamily
Similarity search - Domain/homology
Chem-TZQ / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme
CitationJournal: To Be Published
Title: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA)from Pseudomonas aeruginosa in complex with DDD00082063
Authors: Naismith, J.H. / Moynie, L. / Robinson, D.A.
History
DepositionJan 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)95,19610
Polymers93,8435
Non-polymers1,3535
Water90150
1
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules

A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0784
Polymers37,5372
Non-polymers5412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3340 Å2
ΔGint-17 kcal/mol
Surface area13080 Å2
MethodPISA
2
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0784
Polymers37,5372
Non-polymers5412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-16 kcal/mol
Surface area13560 Å2
MethodPISA
3
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0784
Polymers37,5372
Non-polymers5412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-16 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.885, 144.299, 76.517
Angle α, β, γ (deg.)90.000, 116.260, 90.000
Int Tables number5
Space group name H-MC121
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 - 1652 - 165
21PHEPHEBB2 - 1652 - 165
12PHEPHEAA2 - 1652 - 165
22PHEPHECC2 - 1652 - 165
13PHEPHEAA2 - 1652 - 165
23PHEPHEDD2 - 1652 - 165
14PHEPHEAA2 - 1652 - 165
24PHEPHEEE2 - 1652 - 165
15SERSERBB2 - 1702 - 170
25SERSERCC2 - 1702 - 170
16SERSERBB2 - 1702 - 170
26SERSERDD2 - 1702 - 170
17THRTHRBB2 - 1662 - 166
27THRTHREE2 - 1662 - 166
18SERSERCC2 - 1702 - 170
28SERSERDD2 - 1702 - 170
19THRTHRCC2 - 1662 - 166
29THRTHREE2 - 1662 - 166
110THRTHRDD2 - 1662 - 166
210THRTHREE2 - 1662 - 166

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

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Components

#1: Protein
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / ...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) / Gene: fabA, PA1610 / Production host: Escherichia coli (E. coli)
References: UniProt: O33877, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, trans-2-decenoyl-[acyl-carrier protein] isomerase
#2: Chemical
ChemComp-TZQ / 5-[(3-chloranyl-4-fluoranyl-phenoxy)methyl]furan-2-carboxylic acid


Mass: 270.641 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H8ClFO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.96→83.85 Å / Num. obs: 59206 / % possible obs: 94.3 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.5
Reflection shellResolution: 1.96→2.11 Å / Rmerge(I) obs: 0.856 / Num. unique obs: 2960 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CL6

4cl6


Resolution: 1.96→83.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.064 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 2885 4.9 %RANDOM
Rwork0.2098 ---
obs0.2108 56392 69.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.85 Å2 / Biso mean: 41.314 Å2 / Biso min: 23.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.02 Å2
2--0.09 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.96→83.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 0 90 50 6524
Biso mean--46.46 35.22 -
Num. residues----830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136625
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176153
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6538959
X-RAY DIFFRACTIONr_angle_other_deg1.2971.58714211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7985821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80921.522335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.026151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1341546
X-RAY DIFFRACTIONr_chiral_restr0.0690.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021471
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50310.03
12B50310.03
21A50250.04
22C50250.04
31A49760.05
32D49760.05
41A50450.03
42E50450.03
51B51060.05
52C51060.05
61B50930.05
62D50930.05
71B50490.02
72E50490.02
81C50520.07
82D50520.07
91C50530.04
92E50530.04
101D49850.05
102E49850.05
LS refinement shellResolution: 1.96→1.966 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.282 6 -
Rwork-107 -
obs--1.78 %

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