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- PDB-1esc: THE MOLECULAR MECHANISM OF ENANTIORECOGNITION BY ESTERASES -

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Basic information

Entry
Database: PDB / ID: 1esc
TitleTHE MOLECULAR MECHANISM OF ENANTIORECOGNITION BY ESTERASES
ComponentsESTERASE
KeywordsHYDROLASE (SERINE ESTERASE)
Function / homology
Function and homology information


triglyceride catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triacylglycerol lipase activity / extracellular region
Similarity search - Function
Streptomyces scabies esterase-like / 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
Biological speciesStreptomyces scabiei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWei, Y. / Schottel, J.L. / Derewenda, U. / Swenson, L. / Patkar, S. / Derewenda, Z.S.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: A novel variant of the catalytic triad in the Streptomyces scabies esterase.
Authors: Wei, Y. / Schottel, J.L. / Derewenda, U. / Swenson, L. / Patkar, S. / Derewenda, Z.S.
#1: Journal: To be Published
Title: Crystal Structure of the Streptomyces Scabies Esterase: Reassessment of the Chymotrypsin Paradigm
Authors: Wei, Y. / Schottel, J.L. / Derewenda, U. / Swenson, L. / Patkar, S. / Derewenda, Z.S.
History
DepositionOct 7, 1994Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESTERASE


Theoretical massNumber of molelcules
Total (without water)33,0041
Polymers33,0041
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12700 Å2
Unit cell
Length a, b, c (Å)131.025, 48.501, 70.307
Angle α, β, γ (deg.)90.00, 118.09, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 23
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

21A-491-

HOH

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Components

#1: Protein ESTERASE


Mass: 33003.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces scabiei (bacteria) / References: UniProt: P22266
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop / Details: Green, R., (1992) J. Mol. Biol., 227, 569.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
245 %satammonium sulfate1drop
3100 mMpotassium phosphate1drop
445 %satammonium sulfate1reservoir
5100 mMpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.08 Å / Num. obs: 19449 / % possible obs: 84 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→7.5 Å / σ(F): 0
Details: PHASES WERE CALCULATED FROM FIVE DERIVATIVES. THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD USING FIVE DERIVATIVES.
RfactorNum. reflection
Rwork0.166 -
obs0.166 18098
Refinement stepCycle: LAST / Resolution: 2.1→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 0 223 2519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.08 Å / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0110.02
X-RAY DIFFRACTIONx_angle_d0.0460.04
X-RAY DIFFRACTIONx_planar_d0.050.05
X-RAY DIFFRACTIONx_plane_restr0.0110.02
X-RAY DIFFRACTIONx_chiral_restr0.0960.1

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