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- PDB-6lfb: E. coli Thioesterase I mutant DG -

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Basic information

Entry
Database: PDB / ID: 6lfb
TitleE. coli Thioesterase I mutant DG
ComponentsAcyl-CoA thioesterase I also functions as protease I
KeywordsHYDROLASE / Thioesterase / mutant
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
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: 1.99 Å
AuthorsDeng, X. / Chen, L. / Yang, G.
CitationJournal: Metab. Eng. / Year: 2020
Title: Structure-guided reshaping of the acyl binding pocket of 'TesA thioesterase enhances octanoic acid production in E. coli.
Authors: Deng, X. / Chen, L. / Hei, M. / Liu, T. / Feng, Y. / Yang, G.Y.
History
DepositionDec 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 also functions as protease I


Theoretical massNumber of molelcules
Total (without water)20,0971
Polymers20,0971
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
Unit cell
Length a, b, c (Å)50.786, 50.786, 168.376
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 also functions as protease I / Arylesterase / Multifunctional acyl-CoA thioesterase I/protease I/lysophospholipase L1


Mass: 20096.867 Da / Num. of mol.: 1 / Mutation: E168D,Y171G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J7QCR7, UniProt: P0ADA1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→37.69 Å / Num. obs: 14995 / % possible obs: 93.1 % / Redundancy: 15.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.071 / Net I/σ(I): 20.4
Reflection shellResolution: 1.99→2.09 Å / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1816 / CC1/2: 0.896 / Rpim(I) all: 0.323 / Rrim(I) all: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8U

1u8u


Resolution: 1.99→37.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 11.147 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.169
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25629 714 4.8 %RANDOM
Rwork0.22708 ---
obs0.22843 14178 92.88 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 65.871 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.99→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 21 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191451
X-RAY DIFFRACTIONr_bond_other_d0.0010.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.8771973
X-RAY DIFFRACTIONr_angle_other_deg1.0982.9383112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54924.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79915243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.607159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021618
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02283
X-RAY DIFFRACTIONr_mcbond_it1.3094.199715
X-RAY DIFFRACTIONr_mcbond_other1.3084.196714
X-RAY DIFFRACTIONr_mcangle_it2.066.289892
X-RAY DIFFRACTIONr_mcangle_other2.0596.293893
X-RAY DIFFRACTIONr_scbond_it1.414.452736
X-RAY DIFFRACTIONr_scbond_other1.414.445734
X-RAY DIFFRACTIONr_scangle_other2.2716.5891081
X-RAY DIFFRACTIONr_long_range_B_refined3.749.4221608
X-RAY DIFFRACTIONr_long_range_B_other3.69249.3531606
LS refinement shellResolution: 1.99→2.039 Å
RfactorNum. reflection% reflection
Rfree0.279 59 -
Rwork0.22 1098 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.909 Å / Origin y: -25.161 Å / Origin z: -9.228 Å
111213212223313233
T0.2582 Å2-0.0721 Å20.0417 Å2-0.0881 Å20.0033 Å2--0.0959 Å2
L2.3064 °2-1.3274 °2-0.3753 °2-2.6927 °20.22 °2--3.3151 °2
S0.2043 Å °0.0178 Å °0.1143 Å °-0.1707 Å °-0.0211 Å °0.1776 Å °-0.5548 Å °-0.2117 Å °-0.1832 Å °

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