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- PDB-1nx9: Acetobacter turbidans alpha-amino acid ester hydrolase S205A muta... -

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Basic information

Entry
Database: PDB / ID: 1nx9
TitleAcetobacter turbidans alpha-amino acid ester hydrolase S205A mutant complexed with ampicillin
Componentsalpha-amino acid ester hydrolase
KeywordsHYDROLASE / alpha/beta hydrolase / jellyroll
Function / homology
Function and homology information


alpha-amino-acid esterase / alpha-amino-acid esterase activity / dipeptidyl-peptidase activity
Similarity search - Function
alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AIC / Alpha-amino acid ester hydrolase
Similarity search - Component
Biological speciesAcetobacter pasteurianus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBarends, T.R.M. / Polderman-Tijmes, J.J. / Jekel, P.A. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Acetobacter turbidans {alpha}-Amino Acid Ester Hydrolase: HOW A SINGLE MUTATION IMPROVES AN ANTIBIOTIC-PRODUCING ENZYME.
Authors: Barends, T.R.M. / Polderman-Tijmes, J.J. / Jekel, P.A. / Williams, C. / Wybenga, G. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-amino acid ester hydrolase
B: alpha-amino acid ester hydrolase
C: alpha-amino acid ester hydrolase
D: alpha-amino acid ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,49212
Polymers291,7264
Non-polymers1,7668
Water40,1552229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19020 Å2
ΔGint-41 kcal/mol
Surface area82060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)341.828, 341.828, 341.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
alpha-amino acid ester hydrolase


Mass: 72931.469 Da / Num. of mol.: 4 / Mutation: S205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter pasteurianus (bacteria) / Plasmid: pBADAtS205AMyc-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8VRK8, alpha-amino-acid esterase
#2: Chemical
ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID / Ampicillin


Mass: 349.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H19N3O4S / Comment: antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2229 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate buffer, sodium ampicillin, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.3 Msodium cirtate1reservoirpH5.6
313-14 %PEG40001reservoir
410 mMsodium ampicillin1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8463 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 2002 / Details: premirror, triangular monochromator, bent mirror
RadiationMonochromator: triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8463 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. all: 322911 / Num. obs: 322911 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.081 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Rsym value: 0.322 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 84.3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.768 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.119 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18386 16078 5 %RANDOM
Rwork0.16608 ---
all0.16698 322911 --
obs0.16618 304675 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.609 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19528 0 120 2229 21877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02120292
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.93527728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2152464
X-RAY DIFFRACTIONr_chiral_restr0.0750.22868
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216172
X-RAY DIFFRACTIONr_nbd_refined0.1720.39512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.52026
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.533
X-RAY DIFFRACTIONr_mcbond_it1.3091.512360
X-RAY DIFFRACTIONr_mcangle_it2.212220000
X-RAY DIFFRACTIONr_scbond_it3.64237932
X-RAY DIFFRACTIONr_scangle_it5.2864.57720
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 1230
Rwork0.21 22491
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.184 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.1

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