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- PDB-7bk9: Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehyd... -

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Basic information

Entry
Database: PDB / ID: 7bk9
TitleCrystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with DDD00078426
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-U0W / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMoynie, L. / Naismith, J.H. / Robinson, D.A.
Funding support1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme
CitationJournal: To Be Published
Title: Crystal structures of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa
Authors: Naismith, J.H. / Moynie, L. / Robinson, D.A.
History
DepositionJan 15, 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
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,65112
Polymers93,8435
Non-polymers1,8087
Water2,900161
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)38,0544
Polymers37,5372
Non-polymers5172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3350 Å2
ΔGint-19 kcal/mol
Surface area13520 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)38,3125
Polymers37,5372
Non-polymers7753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-17 kcal/mol
Surface area13550 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)38,3125
Polymers37,5372
Non-polymers7753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-16 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.640, 143.500, 77.780
Angle α, β, γ (deg.)90.000, 114.080, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23C
14A
24E
15B
25D
16B
26C
17B
27E
18D
28C
19D
29E
110C
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 - 1652 - 165
22PHEPHEDC2 - 1652 - 165
13PHEPHEAA2 - 1652 - 165
23PHEPHECD2 - 1652 - 165
14PHEPHEAA2 - 1712 - 171
24PHEPHEEE2 - 1712 - 171
15PHEPHEBB2 - 1652 - 165
25PHEPHEDC2 - 1652 - 165
16PHEPHEBB2 - 1652 - 165
26PHEPHECD2 - 1652 - 165
17PHEPHEBB2 - 1712 - 171
27PHEPHEEE2 - 1712 - 171
18THRTHRDC2 - 1662 - 166
28THRTHRCD2 - 1662 - 166
19PHEPHEDC2 - 1652 - 165
29PHEPHEEE2 - 1652 - 165
110PHEPHECD2 - 1652 - 165
210PHEPHEEE2 - 1652 - 165

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 (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
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-U0W / 5-[(2,3-Dihydro-1H-inden-5-yloxy)methyl]-2-furoic acid / 5-(2,3-dihydro-1~{H}-inden-5-yloxymethyl)furan-2-carboxylic acid / 5-(indan-5-yloxymethyl)furan-2-carboxylic acid / 5-(Indan-5-yloxymethyl)-furan-2-carboxylic acid / 5-[(2,3-dihydro-1H-inden-5-yloxy)methyl]furan-2-carboxylic acid


Mass: 258.269 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C15H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 4000, Ammonium sulfate, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→66.08 Å / Num. obs: 83719 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.6
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4174 / CC1/2: 0.456

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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: 1.94→66.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.503 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 4229 5.1 %RANDOM
Rwork0.1994 ---
obs0.2008 79490 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.9 Å2 / Biso mean: 43.3 Å2 / Biso min: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å21.55 Å2
2---3.07 Å20 Å2
3---0.91 Å2
Refinement stepCycle: final / Resolution: 1.94→66.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 133 161 6725
Biso mean--52.43 44.27 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136740
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176265
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6659119
X-RAY DIFFRACTIONr_angle_other_deg1.3861.60314470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5045828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38821.349341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.987151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4461548
X-RAY DIFFRACTIONr_chiral_restr0.0770.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021513
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50940.06
12B50940.06
21A49450.07
22D49450.07
31A49800.05
32C49800.05
41A50680.07
42E50680.07
51B50510.06
52D50510.06
61B49920.05
62C49920.05
71B50350.07
72E50350.07
81D49950.06
82C49950.06
91D49030.06
92E49030.06
101C49090.07
102E49090.07
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 330 -
Rwork0.325 5873 -
all-6203 -
obs--99.9 %

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