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- PDB-4qd7: Crystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4qd7
TitleCrystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa
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
Putative esterase PA1618
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.765 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

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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


Theoretical massNumber of molelcules
Total (without water)100,8866
Polymers100,8866
Non-polymers00
Water11,295627
1
A: Thioesterase PA1618

A: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,6292
Polymers33,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2540 Å2
ΔGint-18 kcal/mol
Surface area12250 Å2
MethodPISA
2
B: Thioesterase PA1618

B: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,6292
Polymers33,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area2460 Å2
ΔGint-17 kcal/mol
Surface area12500 Å2
MethodPISA
3
C: Thioesterase PA1618
D: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,6292
Polymers33,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-17 kcal/mol
Surface area12740 Å2
MethodPISA
4
E: Thioesterase PA1618
F: Thioesterase PA1618


Theoretical massNumber of molelcules
Total (without water)33,6292
Polymers33,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-16 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.652, 202.514, 90.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Thioesterase PA1618


Mass: 16814.395 Da / Num. of mol.: 6 / Fragment: Hotdog domain
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.32 Å3/Da / Density % sol: 47 %
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: 0.97939 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.72→35.87 Å / Num. obs: 97075 / % possible obs: 97.94 % / 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
autoXDSdata reduction
autoXDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.765→35.869 Å / SU ML: 0.2 / σ(F): 1.09 / Phase error: 26.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1892 2.06 %RANDOM
Rwork0.2066 ---
obs0.207 91813 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.765→35.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 0 627 6854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086543
X-RAY DIFFRACTIONf_angle_d1.1598897
X-RAY DIFFRACTIONf_dihedral_angle_d13.9192385
X-RAY DIFFRACTIONf_chiral_restr0.0741029
X-RAY DIFFRACTIONf_plane_restr0.0051157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.765-1.80910.31871320.30556255X-RAY DIFFRACTION98
1.8091-1.85810.31911350.27726426X-RAY DIFFRACTION100
1.8581-1.91270.30481330.26366376X-RAY DIFFRACTION100
1.9127-1.97450.25961330.23856319X-RAY DIFFRACTION100
1.9745-2.0450.24611350.21986399X-RAY DIFFRACTION99
2.045-2.12690.24211350.21466402X-RAY DIFFRACTION100
2.1269-2.22370.2561350.21386400X-RAY DIFFRACTION100
2.2237-2.34090.24651340.21446395X-RAY DIFFRACTION100
2.3409-2.48750.27161350.21096388X-RAY DIFFRACTION99
2.4875-2.67950.22681350.21096452X-RAY DIFFRACTION100
2.6795-2.94910.24211360.20896427X-RAY DIFFRACTION100
2.9491-3.37550.19551360.19676466X-RAY DIFFRACTION99
3.3755-4.25170.1861370.17056535X-RAY DIFFRACTION100
4.2517-35.87680.18311410.18476681X-RAY DIFFRACTION99

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