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- PDB-5tid: X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y1... -

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Basic information

Entry
Database: PDB / ID: 5tid
TitleX-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 5 in complex with octanoic acid
ComponentsAcyl-CoA thioesterase I
KeywordsHYDROLASE / Thioesterase / TesA / fatty acid / octanoic acid
Function / homology
Function and homology information


arylesterase / lysophospholipase / palmitoyl-CoA hydrolase / long-chain fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / phosphatidylcholine lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity / lipid metabolic process ...arylesterase / lysophospholipase / palmitoyl-CoA hydrolase / long-chain fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / phosphatidylcholine lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity / lipid metabolic process / peptidase activity / outer membrane-bounded 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsThoden, J.B. / Holden, H.M. / Grisewood, M.J. / Hernandez Lozada, N.J. / Gifford, N.P. / Mendez-Perez, D. / Schoenberger, H.A. / Allan, M.F. / Pfleger, B.F. / Marines, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: ACS Catal / Year: 2017
Title: Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.
Authors: Grisewood, M.J. / Hernandez Lozada, N.J. / Thoden, J.B. / Gifford, N.P. / Mendez-Perez, D. / Schoenberger, H.A. / Allan, M.F. / Floy, M.E. / Lai, R.Y. / Holden, H.M. / Pfleger, B.F. / Maranas, C.D.
History
DepositionOct 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,8302
Polymers20,6861
Non-polymers1441
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.716, 55.177, 42.330
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20685.525 Da / Num. of mol.: 1 / Fragment: UNP residues 28-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tesA, apeA, pldC, b0494, JW0483 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P0ADA1, Hydrolases; Acting on ester bonds; Thioester hydrolases, lysophospholipase
#2: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


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


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20-25% PEG-5000, 100 mM homopipes, 3 mM octanoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 16, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 56148 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 13.2
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIC

5tic


Resolution: 1.2→40.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.58 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17746 2879 5.1 %RANDOM
Rwork0.15832 ---
obs0.15929 53269 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.2 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.2→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 10 334 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021499
X-RAY DIFFRACTIONr_bond_other_d00.021468
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9742043
X-RAY DIFFRACTIONr_angle_other_deg0.83833385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5724.9371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17215261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.042159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2690.817725
X-RAY DIFFRACTIONr_mcbond_other1.2440.812724
X-RAY DIFFRACTIONr_mcangle_it1.8871.221908
X-RAY DIFFRACTIONr_mcangle_other1.8921.226909
X-RAY DIFFRACTIONr_scbond_it3.2181.166774
X-RAY DIFFRACTIONr_scbond_other3.2161.167775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9591.611129
X-RAY DIFFRACTIONr_long_range_B_refined6.6229.8442139
X-RAY DIFFRACTIONr_long_range_B_other6.2048.1541850
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 231 -
Rwork0.256 3607 -
obs--93.16 %

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