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- PDB-1c8u: CRYSTAL STRUCTURE OF THE E.COLI THIOESTERASE II, A HOMOLOGUE OF T... -

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Basic information

Entry
Database: PDB / ID: 1c8u
TitleCRYSTAL STRUCTURE OF THE E.COLI THIOESTERASE II, A HOMOLOGUE OF THE HUMAN NEF-BINDING ENZYME
ComponentsACYL-COA THIOESTERASE II
KeywordsHYDROLASE / INTERNAL REPEATS
Function / homology
Function and homology information


acyl-CoA hydrolase / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Acyl-CoA thioesterase / Acyl-CoA thioesterase II domain / Acyl-CoA thioesterase / Acyl-CoA thioesterase, double hotdog domain / : / Acyl-CoA thioesterase N-terminal domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA thioesterase 2 / Acyl-CoA thioesterase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLi, J. / Derewenda, Z.S.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme.
Authors: Li, J. / Derewenda, U. / Dauter, Z. / Smith, S. / Derewenda, Z.S.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Thioesterase II from Escherichia Coli
Authors: Swenson, L. / Green, R. / Smith, S. / Derewenda, Z.S.
History
DepositionJul 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: ACYL-COA THIOESTERASE II
B: ACYL-COA THIOESTERASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2054
Polymers63,7462
Non-polymers4592
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-12 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.902, 119.805, 165.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein ACYL-COA THIOESTERASE II / E.C.3.1.2.-


Mass: 31873.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: MODIFIED PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23911, UniProt: P0AGG2*PLUS, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NACL, NAOAC, LDAO, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
220 mMTris-HCl1drop
32 M1reservoirNaCl
4100 mM1reservoirNaOAc
55 mMLDAO1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 74901 / Num. obs: 74732 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.425 / % possible all: 99.4
Reflection
*PLUS
Num. obs: 74901 / % possible obs: 99.7 % / Num. measured all: 353158
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1125 1.5 %RANDOM
Rwork0.2176 ---
all0.2303 74732 --
obs0.2303 74732 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 32 535 5073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.248 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

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