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- PDB-1qz3: CRYSTAL STRUCTURE OF MUTANT M211S/R215L OF CARBOXYLESTERASE EST2 ... -

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Basic information

Entry
Database: PDB / ID: 1qz3
TitleCRYSTAL STRUCTURE OF MUTANT M211S/R215L OF CARBOXYLESTERASE EST2 COMPLEXED WITH HEXADECANESULFONATE
ComponentsCARBOXYLESTERASE EST2
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD
Function / homology
Function and homology information


Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-HEXADECANOSULFONIC ACID / Hydrolase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe Simone, G. / Mandrich, L. / Menchise, V. / Giordano, V. / Febbraio, F. / Rossi, M. / Pedone, C. / Manco, G.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: A substrate-induced switch in the reaction mechanism of a thermophilic esterase: kinetic evidences and structural basis.
Authors: De Simone, G. / Mandrich, L. / Menchise, V. / Giordano, V. / Febbraio, F. / Rossi, M. / Pedone, C. / Manco, G.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: A SNAPSHOT OF THE TRANSITION STATE ANALOGUE OF A NOVEL THERMOPHILIC ESTERASE BELONGING TO THE SUBFAMILY OF MAMMALIAN HORMONE-SENSITIVE LIPASE
Authors: DE SIMONE, G. / GALDIERO, S. / MANCO, G. / LANG, D. / ROSSI, M. / PEDONE, C.
History
DepositionSep 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / entity_src_gen / pdbx_database_remark / struct_ref / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_ec ..._diffrn_source.pdbx_synchrotron_site / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CARBOXYLESTERASE EST2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5572
Polymers34,2511
Non-polymers3071
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.193, 85.193, 103.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CARBOXYLESTERASE EST2


Mass: 34250.820 Da / Num. of mol.: 1 / Mutation: R215L, M211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Plasmid: PT7-7SCII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIG1
#2: Chemical ChemComp-HDS / 1-HEXADECANOSULFONIC ACID


Mass: 306.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: AMMONIUM SULPHATE, TRIS BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Mammonium sulfate1reservoir
20.1 MTris1reservoirpH8.5
320 mMphosphate1drop
44 %(v/v)acetonitrile1drop
50.015 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 17707 / % possible obs: 98.8 % / Rsym value: 0.089 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.426 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 177515 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.426

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVQ

1evq


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 789 4.5 %RANDOM
Rwork0.174 ---
obs0.188 16467 94.1 %-
all-17707 --
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 19 253 2684
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_mcbond_it1.1751.5
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_mcangle_it1.8352
X-RAY DIFFRACTIONc_scangle_it3.1372.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1p_hep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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