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- PDB-4qd9: Crystal structure of Thioesterase PA1618 from Pseudomonas aerugin... -

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Basic information

Entry
Database: PDB / ID: 4qd9
TitleCrystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa in complex with benzoyl-dO-CoA
ComponentsThioesterase PA1618
KeywordsHYDROLASE / Hotdog Fold / Thioesterase / Coenzyme A / acyl carrier protein / cytosol
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / menaquinone biosynthetic process / peroxisome / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
benzoyl-oxydephosphocoenzyme A / Putative esterase PA1618
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.767 Å
AuthorsJi, T. / Allen, K.N. / Dunaway-Mariano, D.
CitationJournal: To be Published
Title: Design and Use of an Ester Analog of CoA to Trap the Michaelis Complex in a Thioesterase
Authors: Latham, J.A. / Ji, T. / Matthews, K. / Allen, K.N. / Dunaway-Mariano, D.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioesterase PA1618
B: Thioesterase PA1618
C: Thioesterase PA1618
D: Thioesterase PA1618
E: Thioesterase PA1618
F: Thioesterase PA1618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3128
Polymers99,7616
Non-polymers1,5512
Water11,908661
1
A: Thioesterase PA1618

A: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,2542
Polymers33,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2590 Å2
ΔGint-19 kcal/mol
Surface area12550 Å2
2
B: Thioesterase PA1618

B: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,2542
Polymers33,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
3
C: Thioesterase PA1618
D: Thioesterase PA1618
E: Thioesterase PA1618
F: Thioesterase PA1618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0586
Polymers66,5074
Non-polymers1,5512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.026, 201.490, 91.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-261-

HOH

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Components

#1: Protein
Thioesterase PA1618


Mass: 16626.814 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1618 / Plasmid: pET23-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I3A4, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-31B / benzoyl-oxydephosphocoenzyme A / benzoyl-OdCoA


Mass: 775.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 45% PEG400, 0.1M Bis Tris, 10mM beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.72→37.53 Å / Num. obs: 98312 / % possible obs: 97.85 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
autoXDSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.767→37.529 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1889 2.04 %
Rwork0.1863 --
obs0.1871 92801 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.767→37.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 104 661 7095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076569
X-RAY DIFFRACTIONf_angle_d1.168931
X-RAY DIFFRACTIONf_dihedral_angle_d18.2992457
X-RAY DIFFRACTIONf_chiral_restr0.0761017
X-RAY DIFFRACTIONf_plane_restr0.0051145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.767-1.81480.30511410.24376760X-RAY DIFFRACTION97
1.8148-1.86820.27871440.21356971X-RAY DIFFRACTION100
1.8682-1.92850.26421440.23196921X-RAY DIFFRACTION99
1.9285-1.99740.21981450.19996982X-RAY DIFFRACTION100
1.9974-2.07740.25081430.1986876X-RAY DIFFRACTION99
2.0774-2.17190.22431450.19226980X-RAY DIFFRACTION100
2.1719-2.28640.23321460.19426963X-RAY DIFFRACTION99
2.2864-2.42960.23021440.19416997X-RAY DIFFRACTION100
2.4296-2.61720.23261440.19676956X-RAY DIFFRACTION99
2.6172-2.88050.26421470.19477046X-RAY DIFFRACTION100
2.8805-3.29710.21061470.19437031X-RAY DIFFRACTION99
3.2971-4.15310.21581470.16187124X-RAY DIFFRACTION100
4.1531-37.53770.18781520.1667305X-RAY DIFFRACTION99

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