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

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Basic information

Entry
Database: PDB / ID: 7bhj
TitleCrystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with DDD00084774
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / FabA / PA1610 / Complex
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 domain superfamily
Similarity search - Domain/homology
Chem-TQH / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Commission United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA)from Pseudomonas aeruginosa in complex with DDD00084774
Authors: Moynie, L. / Naismith, J.H. / Robinson, D.A.
History
DepositionJan 11, 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)94,8849
Polymers93,8435
Non-polymers1,0414
Water84747
1
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

A: 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_555-x,y,-z1
Buried area3230 Å2
ΔGint-17 kcal/mol
Surface area13780 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)38,0584
Polymers37,5372
Non-polymers5212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-18 kcal/mol
Surface area13210 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)38,0584
Polymers37,5372
Non-polymers5212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-19 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.420, 142.200, 78.430
Angle α, β, γ (deg.)90.000, 114.680, 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: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA2 - 1652 - 165
21PHEPHEBB2 - 1652 - 165
12PHEPHEAA2 - 1712 - 171
22PHEPHECC2 - 1712 - 171
13SERSERAA2 - 1672 - 167
23SERSERDD2 - 1672 - 167
14PHEPHEAA2 - 1712 - 171
24PHEPHEEE2 - 1712 - 171
15PHEPHEBB2 - 1652 - 165
25PHEPHECC2 - 1652 - 165
16THRTHRBB2 - 1662 - 166
26THRTHRDD2 - 1662 - 166
17PHEPHEBB2 - 1652 - 165
27PHEPHEEE2 - 1652 - 165
18SERSERCC2 - 1672 - 167
28SERSERDD2 - 1672 - 167
19PHEPHECC2 - 1712 - 171
29PHEPHEEE2 - 1712 - 171
110SERSERDD2 - 1672 - 167
210SERSEREE2 - 1672 - 167

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-TQH / ~{N}-[(5-methylfuran-2-yl)methyl]-5-thiophen-2-yl-4~{H}-1,2,4-triazol-3-amine


Mass: 260.315 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C12H12N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 8000, Magnesium chloride, Tris-HcL

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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 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.11→66.5 Å / Num. obs: 65125 / % possible obs: 99.6 % / Redundancy: 4.05 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.68
Reflection shellResolution: 2.11→2.15 Å / Rmerge(I) obs: 1.298 / Num. unique obs: 3225 / CC1/2: 0.446

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Processing

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

4cl6


Resolution: 2.11→66.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.519 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 3287 5 %RANDOM
Rwork0.2024 ---
obs0.204 61836 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.82 Å2 / Biso mean: 54.454 Å2 / Biso min: 33.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å21.21 Å2
2---0.14 Å20 Å2
3----2.37 Å2
Refinement stepCycle: final / Resolution: 2.11→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 0 72 47 6588
Biso mean--87.4 49.73 -
Num. residues----839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136700
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176238
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6519061
X-RAY DIFFRACTIONr_angle_other_deg1.2891.58914399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7325832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68621.374342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.649151077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5071548
X-RAY DIFFRACTIONr_chiral_restr0.070.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021510
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A49960.04
12B49960.04
21A52180.05
22C52180.05
31A50690.06
32D50690.06
41A51110.06
42E51110.06
51B50420.03
52C50420.03
61B50410.03
62D50410.03
71B49850.04
72E49850.04
81C51100.05
82D51100.05
91C51460.04
92E51460.04
101D50130.06
102E50130.06
LS refinement shellResolution: 2.11→2.165 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 249 -
Rwork0.345 4577 -
all-4826 -
obs--99.98 %

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