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- PDB-1ivn: E.coli Thioesterase I/Protease I/Lysophospholiase L1 -

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Basic information

Entry
Database: PDB / ID: 1ivn
TitleE.coli Thioesterase I/Protease I/Lysophospholiase L1
ComponentsThioesterase I
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


: / : / : / : / phospholipase B activity / : / arylesterase / lysophospholipase / palmitoyl-CoA hydrolase / long-chain fatty acyl-CoA hydrolase activity ...: / : / : / : / phospholipase B activity / : / 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 / 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: 1.9 Å
AuthorsLo, Y.-C. / Shaw, J.-F. / Liaw, Y.-C.
CitationJournal: 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
DepositionMar 27, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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: Thioesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7503
Polymers21,5611
Non-polymers1882
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Thioesterase I
hetero molecules

A: Thioesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4996
Polymers43,1232
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2010 Å2
ΔGint-48 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.936, 49.936, 170.364
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 Thioesterase I / Acyl-CoA 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(+) / Production host: Escherichia coli (E. coli) / 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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.41 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2-[N-morpholino]ethanesulfonic acid, PEGMME 5000, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124.5 mg/mlprotein11
210 mMsodium phosphate12pH7.0
325.5 %(w/w)PEG5000 MME12

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9236 Å / Relative weight: 1
ReflectionResolution: 1.9→28.15 Å / Num. all: 17352 / Num. obs: 17352 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.96 % / Biso Wilson estimate: 26.6 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 18 / Limit k min: 0 / Limit l max: 88 / Limit l min: 0 / Observed criterion F max: 706205.76 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 4.94 / % possible all: 87.2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 28.1 Å / Num. obs: 17893 / Redundancy: 21 %
Reflection shell
*PLUS
Lowest resolution: 2 Å

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Processing

Software
NameVersionClassificationNB
CNS1refinement
ADSC(QUANTUM)data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JRL

1jrl


Resolution: 1.9→28.15 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
Rfree0.255 1695 10 %RANDOM
Rwork0.229 ---
all-17893 --
obs-16976 94.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.2166 Å2 / ksol: 0.383183 e/Å3
Displacement parametersBiso max: 98.63 Å2 / Biso mean: 46.8 Å2 / Biso min: 22.55 Å2
Baniso -1Baniso -2Baniso -3
1-8.73 Å20 Å20 Å2
2--8.73 Å20 Å2
3----17.46 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.27 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 11 147 1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_improper_angle_d0.79
X-RAY DIFFRACTIONx_mcbond_it1.641.5
X-RAY DIFFRACTIONx_mcangle_it2.752
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it3.062.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-2.020.3132257.70.32422120.0222909243783.7
2.02-2.170.342548.70.28325780.0182923283296.9
2.17-2.390.2929510.10.25125770.0152925287298.2
2.39-2.740.28630210.20.2426040.0142952290698.4
2.74-3.450.28331810.60.24426380.0142989295698.9
3.45-28.150.2633019.40.22226720.0133209297392.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4imd.paramimd.top
X-RAY DIFFRACTION5gol.paramgol.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 28.1 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Lowest resolution: 2 Å

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