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- PDB-1evq: THE CRYSTAL STRUCTURE OF THE THERMOPHILIC CARBOXYLESTERASE EST2 F... -

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Basic information

Entry
Database: PDB / ID: 1evq
TitleTHE CRYSTAL STRUCTURE OF THE THERMOPHILIC CARBOXYLESTERASE EST2 FROM ALICYCLOBACILLUS ACIDOCALDARIUS
ComponentsSERINE HYDROLASE
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
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsDe Simone, G. / Galdiero, S. / Manco, G. / Lang, D. / Rossi, M. / Pedone, C.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: A snapshot of a 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Diffraction Studies of the Carboxylesterase EST2 from Alicyclobacillus acidocaldarius
Authors: De Simone, G. / Manco, G. / Galdiero, S. / Lombardi, A. / Rossi, M. / Pavone, V.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal Structure of Brefeldin A Esterase, a Bacterial Homolog of the Mammalian Hormone-sensitive Lipase
Authors: Wei, Y. / Contreras, J.A. / Sheffield, P. / Osterlund, T. / Derewenda, U. / Kneusel, R.E. / Matern, U. / Holm, C. / Derewenda, Z.S.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / 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 / _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

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Assembly

Deposited unit
A: SERINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8873
Polymers34,5271
Non-polymers3602
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.105, 79.105, 107.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-401-

TRS

DetailsThe biological assembly is a monomer

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Components

#1: Protein SERINE HYDROLASE


Mass: 34526.551 Da / Num. of mol.: 1
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, carboxylesterase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 48.8 %
Description: Wavelength 0.9785 is the peak wavelength, 0.9786 is the inflection, and 0.9810 is remote.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 2% PEG 400, 100mM Hepes pH 7.8, 2M Ammonium Sulphate, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMTris-HCl1drop
20.1 M1dropNaCl
32.5 mM1dropMgCl2
44 mg/mlprotein1drop
52 Mammonium sulfate1reservoir
6100 mMHEPES1reservoir
72 %PEG4001reservoir
81 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9785, 0.9786, 0.9810
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 10, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97861
30.9811
ReflectionResolution: 2.6→100 Å / Num. all: 203297 / Num. obs: 10886 / % possible obs: 99.4 % / Redundancy: 18 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.236 / Num. unique all: 1057 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 8.8

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 515 5 %RANDOM
Rwork0.216 ---
all-10753 --
obs-10753 98 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 22 78 2523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6

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