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- PDB-1v2g: The L109P mutant of E. coli Thioesterase I/Protease I/Lysophospho... -

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Basic information

Entry
Database: PDB / ID: 1v2g
TitleThe L109P mutant of E. coli Thioesterase I/Protease I/Lysophospholipase L1 (TAP) in complexed with octanoic acid
ComponentsAcyl-CoA thioesterase I
KeywordsHYDROLASE / SGNH-hydrolase fold
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
IMIDAZOLE / 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 Å
AuthorsLo, Y.-C. / Lin, S.-C. / Liaw, Y.-C.
Citation
Journal: 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.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network
Authors: Lo, Y.-C. / Lin, S.-C. / Shaw, J.-F. / Liaw, Y.-C.
History
DepositionOct 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)21,8554
Polymers21,5451
Non-polymers3093
Water1,928107
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)43,7098
Polymers43,0912
Non-polymers6196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2850 Å2
ΔGint-19.6 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.978, 49.978, 171.491
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


Mass: 21545.371 Da / Num. of mol.: 1 / Mutation: L109P
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-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.49 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2-[N-morpholino]ethanesulfonic acid, PEGMME5K, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.1272 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: May 30, 2000
RadiationMonochromator: Si111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2→24.81 Å / Num. all: 15163 / Num. obs: 14724 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 32.7 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 17 / Limit k min: 0 / Limit l max: 85 / Limit l min: 0 / Observed criterion F max: 1110446.57 / Observed criterion F min: 0.77 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.2 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
XPRESSdata reduction
DIP2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JRL

1jrl


Resolution: 2→24.81 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1437 10.2 %Random
Rwork0.225 ---
all-15512 --
obs-14138 91.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 54.3254 Å2 / ksol: 0.338479 e/Å3
Displacement parametersBiso max: 118.63 Å2 / Biso mean: 51.16 Å2 / Biso min: 27.53 Å2
Baniso -1Baniso -2Baniso -3
1-10.6 Å20 Å20 Å2
2--10.6 Å20 Å2
3----21.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.36 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 20 107 1537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_torsion_deg21.6
X-RAY DIFFRACTIONc_torsion_impr_deg0.86
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 (%)
2-2.090.39816410.80.37713570.0311875152181.1
2.09-2.20.3771559.40.30614980.031886165387.6
2.2-2.340.2981639.60.26715420.0231889170590.3
2.34-2.520.3411749.70.26316210.0261919179593.5
2.52-2.770.3241628.70.25117010.0251933186396.4
2.77-3.170.31519810.70.24716530.0221923185196.2
3.17-3.990.25819010.20.22216640.0191973185493.9
3.99-24.810.21823112.20.19316650.0142124189689.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2imd.paramimd.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5oct.paramoct.top

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