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- PDB-1u8u: E. coli Thioesterase I/Protease I/Lysophospholiase L1 in complexe... -

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Basic information

Entry
Database: PDB / ID: 1u8u
TitleE. coli Thioesterase I/Protease I/Lysophospholiase L1 in complexed with octanoic acid
ComponentsAcyl-CoA thioesterase I
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / : / palmitoyl-CoA hydrolase / : / : / : / : / fatty acyl-CoA hydrolase activity ...arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / : / palmitoyl-CoA hydrolase / : / : / : / : / fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity / lipid metabolic process / outer membrane-bounded periplasmic space / peptidase activity / periplasmic space / proteolysis / identical protein binding
Similarity search - Function
Lipase, GDSL, active site / Lipolytic enzymes "G-D-S-L" family, serine active site. / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OCTANOIC ACID (CAPRYLIC ACID) / Thioesterase 1/protease 1/lysophospholipase L1 / Thioesterase 1/protease 1/lysophospholipase L1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLo, Y.-C. / Lin, S.-C. / Liaw, Y.-C.
CitationJournal: Biochemistry / Year: 2005
Title: Substrate specificities of Escherichia coli thioesterase I/protease I/lysophospholipase L1 are governed by its switch loop movement
Authors: Lo, Y.-C. / Lin, S.-C. / Shaw, J.-F. / Liaw, Y.-C.
History
DepositionAug 7, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Acyl-CoA thioesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0786
Polymers21,5611
Non-polymers5175
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acyl-CoA thioesterase I
hetero molecules

A: Acyl-CoA thioesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,15612
Polymers43,1232
Non-polymers1,03310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4110 Å2
ΔGint-30.3 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.425, 50.425, 172.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Acyl-CoA thioesterase I / Thioesterase I / Protease I / Lysophospholipase L1


Mass: 21561.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tesA, apeA, pldC / Plasmid: pET-20b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P29679, UniProt: P0ADA1*PLUS, lysophospholipase, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 2-[N-morpholino]ethanesulfonic acid, PEGMME5K, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9236 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9236 Å / Relative weight: 1
ReflectionResolution: 2.08→19.78 Å / Num. all: 13812 / Num. obs: 13812 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 28.2 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 17 / Limit k min: 0 / Limit l max: 82 / Limit l min: 0 / Observed criterion F max: 710490.31 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.3
Reflection shellResolution: 2.08→2.17 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.92 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
ADSC(QUANTUM)data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IVN

1ivn


Resolution: 2.08→19.78 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1361 10.3 %Random
Rwork0.228 ---
all-14137 --
obs-13213 93.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 73.857 Å2 / ksol: 0.393248 e/Å3
Displacement parametersBiso max: 153.08 Å2 / Biso mean: 52.94 Å2 / Biso min: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1-10.7 Å20 Å20 Å2
2--10.7 Å20 Å2
3----21.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Luzzati d res high-2.08
Refinement stepCycle: LAST / Resolution: 2.08→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 33 112 1562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.4
X-RAY DIFFRACTIONx_torsion_impr_deg1.03
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.08-2.170.351152100.32713650.0281733151787.5
2.17-2.290.3651539.90.33113950.0291723154889.8
2.29-2.430.3391388.50.28214770.0291717161594
2.43-2.620.31117910.70.25114920.0231735167196.3
2.62-2.880.30218310.80.24715190.0221751170297.2
2.88-3.30.27318810.90.23415390.021767172797.7
3.3-4.150.21317410.10.215500.0161800172495.8
4.15-19.780.23119411.40.215150.0171929170988.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2oct_gol_imd.paramoct_gol_imd.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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