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- PDB-2b4k: Acetobacter turbidans alpha-amino acid ester hydrolase complexed ... -

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Basic information

Entry
Database: PDB / ID: 2b4k
TitleAcetobacter turbidans alpha-amino acid ester hydrolase complexed with phenylglycine
ComponentsAlpha-amino acid ester hydrolase
KeywordsHYDROLASE / alpha-beta hydrolase
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 ...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
D-PHENYLGLYCINE / Alpha-amino acid ester hydrolase
Similarity search - Component
Biological speciesAcetobacter pasteurianus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBarends, T.R.M. / Polderman-Tijmes, J.J. / Jekel, P.A. / Williams, C. / Wybenga, G. / 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. / Polderman-Tijmes, J.J. / Jekel, P.A. / Williams, C. / Wybenga, G. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / 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 / _entity.pdbx_description / _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_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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

Downloads & links

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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)292,61211
Polymers291,7904
Non-polymers8227
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16320 Å2
ΔGint-48 kcal/mol
Surface area81810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)340.909, 340.909, 340.909
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: 72947.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter pasteurianus (bacteria) / Gene: aehA / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8VRK8
#2: Chemical ChemComp-PG9 / D-PHENYLGLYCINE


Type: D-peptide linking / Mass: 151.163 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H9NO2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 6.1 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, PEG4000, phenylglycine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 121384 / Num. obs: 121384 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.186
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.917 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NX9

1nx9


Resolution: 3.3→15 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.813 / SU B: 19.366 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28934 4836 5 %RANDOM
Rwork0.25774 ---
all0.25933 91758 --
obs0.25933 91758 99.38 %-
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: 19.29 Å2
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19532 0 57 5 19594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02120225
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.9327614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8552464
X-RAY DIFFRACTIONr_chiral_restr0.0720.22855
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216117
X-RAY DIFFRACTIONr_nbd_refined0.1980.310883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5811
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.52
LS refinement shellResolution: 3.3→3.381 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 370
Rwork0.308 6498

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