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- PDB-1u4n: Crystal Structure Analysis of the M211S/R215L EST2 mutant -

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Basic information

Entry
Database: PDB / ID: 1u4n
TitleCrystal Structure Analysis of the M211S/R215L EST2 mutant
ComponentsCARBOXYLESTERASE EST2
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD
Function / homologyshort-chain carboxylesterase activity / 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 / Hydrolase
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDe Simone, G. / Menchise, V. / Alterio, V. / Mandrich, L. / Rossi, M. / Manco, G. / Pedone, C.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of an EST2 Mutant Unveils Structural Insights on the H Group of the Carboxylesterase/Lipase Family.
Authors: De Simone, G. / Menchise, V. / Alterio, V. / Mandrich, L. / Rossi, M. / Manco, G. / Pedone, C.
#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.
#2: 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.
History
DepositionJul 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_database_remark / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num ..._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.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Aug 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)34,3472
Polymers34,2511
Non-polymers961
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CARBOXYLESTERASE EST2
hetero molecules

A: CARBOXYLESTERASE EST2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6944
Polymers68,5022
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4650 Å2
ΔGint-73 kcal/mol
Surface area22900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.200, 83.080, 54.030
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 EST2


Mass: 34250.820 Da / Num. of mol.: 1 / Mutation: M211S, R215L
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.9 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris/HCl, 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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 17360 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Rsym value: 0.068 / Net I/σ(I): 20.7
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.208 / % possible all: 87.2

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Processing

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

1evq


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 751 -RANDOM
Rwork0.179 ---
all-17368 --
obs-15102 87.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 4 252 2663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.1→2.15 Å /
RfactorNum. reflection
Rfree0.262 49
Rwork0.199 -

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