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- PDB-2hm7: Crystal Structure Analysis of the G84S EST2 mutant -

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Basic information

Entry
Database: PDB / ID: 2hm7
TitleCrystal Structure Analysis of the G84S EST2 mutant
ComponentsCarboxylesterase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Hydrolase
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMenchise, V. / Alterio, V. / De Simone, G.
Citation
Journal: Proteins / Year: 2007
Title: Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius.
Authors: Mandrich, L. / Menchise, V. / Alterio, V. / De Simone, G. / Pedone, C. / Rossi, M. / 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
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4652
Polymers34,3691
Non-polymers961
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carboxylesterase
hetero molecules

A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9304
Polymers68,7382
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4830 Å2
ΔGint-72 kcal/mol
Surface area22450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.660, 82.170, 47.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carboxylesterase /


Mass: 34368.996 Da / Num. of mol.: 1 / Mutation: G84S
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.82 Å3/Da / Density % sol: 32.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 8000, 0.1M TRIS/HCl, 0.2M MAGNESIUM CHLORIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 17662 / Num. obs: 17662 / % possible obs: 97.8 % / Rsym value: 0.056 / Net I/σ(I): 17.7
Reflection shellHighest resolution: 2 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.137 / % possible all: 80.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVQ

1evq


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.222 882 RANDOM
Rwork0.196 --
obs-17482 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 4 162 2580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006

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