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- PDB-2b9v: Acetobacter turbidans alpha-amino acid ester hydrolase -

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Basic information

Entry
Database: PDB / ID: 2b9v
TitleAcetobacter turbidans alpha-amino acid ester hydrolase
ComponentsAlpha-amino acid ester hydrolase
KeywordsHYDROLASE / catalytic triad / 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
Alpha-amino acid ester hydrolase
Similarity search - Component
Biological speciesAcetobacter pasteurianus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBarends, T.R.M.
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
DepositionOct 13, 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 / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / struct_ref_seq_dif
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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: Alpha-amino acid ester hydrolase
F: Alpha-amino acid ester hydrolase
G: Alpha-amino acid ester hydrolase
H: Alpha-amino acid ester hydrolase
I: Alpha-amino acid ester hydrolase
J: Alpha-amino acid ester hydrolase
K: Alpha-amino acid ester hydrolase
L: Alpha-amino acid ester hydrolase
M: Alpha-amino acid ester hydrolase
N: Alpha-amino acid ester hydrolase
O: Alpha-amino acid ester hydrolase
P: Alpha-amino acid ester hydrolase


Theoretical massNumber of molelcules
Total (without water)1,167,16016
Polymers1,167,16016
Non-polymers00
Water65,8273654
1
A: Alpha-amino acid ester hydrolase
B: Alpha-amino acid ester hydrolase
C: Alpha-amino acid ester hydrolase
D: Alpha-amino acid ester hydrolase


Theoretical massNumber of molelcules
Total (without water)291,7904
Polymers291,7904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-38 kcal/mol
Surface area81430 Å2
MethodPISA, PQS
2
E: Alpha-amino acid ester hydrolase
F: Alpha-amino acid ester hydrolase
G: Alpha-amino acid ester hydrolase
H: Alpha-amino acid ester hydrolase


Theoretical massNumber of molelcules
Total (without water)291,7904
Polymers291,7904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14050 Å2
ΔGint-37 kcal/mol
Surface area81530 Å2
MethodPISA, PQS
3
I: Alpha-amino acid ester hydrolase
J: Alpha-amino acid ester hydrolase
K: Alpha-amino acid ester hydrolase
L: Alpha-amino acid ester hydrolase


Theoretical massNumber of molelcules
Total (without water)291,7904
Polymers291,7904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-37 kcal/mol
Surface area81300 Å2
MethodPISA, PQS
4
M: Alpha-amino acid ester hydrolase
N: Alpha-amino acid ester hydrolase
O: Alpha-amino acid ester hydrolase
P: Alpha-amino acid ester hydrolase


Theoretical massNumber of molelcules
Total (without water)291,7904
Polymers291,7904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint-35 kcal/mol
Surface area81720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.369, 275.594, 197.953
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 50 - 666 / Label seq-ID: 10 - 626

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP

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Components

#1: Protein
Alpha-amino acid ester hydrolase


Mass: 72947.469 Da / Num. of mol.: 16
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): TOP10F / References: UniProt: Q8VRK8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3654 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15-17% PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate buffer, pH 4.6, 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: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 598744 / Num. obs: 598744 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.341 / % possible all: 67.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MPX

1mpx


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, REFINEMENT AGAINST DETWINNED DATA. The structure data contains both detwinned and twinned data.
RfactorNum. reflection% reflectionSelection details
Rfree0.23477 25420 4.8 %RANDOM, BUT SUCH THAT TWIN-RELATED REFLECTIONS ARE ALWAYS IN THE SAME SUBSET
Rwork0.19878 ---
all0.20051 504379 --
obs0.20051 504379 75.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77056 0 0 3654 80710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02279568
X-RAY DIFFRACTIONr_bond_other_d00.0258914
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.938108656
X-RAY DIFFRACTIONr_angle_other_deg3.3863140436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.71559696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46723.5543872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3491511776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.36715528
X-RAY DIFFRACTIONr_chiral_restr0.1050.211232
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0290000
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0216816
X-RAY DIFFRACTIONr_nbd_refined0.1960.39456
X-RAY DIFFRACTIONr_nbd_other0.2340.334971
X-RAY DIFFRACTIONr_nbtor_refined0.1860.525478
X-RAY DIFFRACTIONr_nbtor_other0.1140.524687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5117
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0810.5489
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.3126
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4170.3197
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.511
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2960.55
X-RAY DIFFRACTIONr_mcbond_it1.0661.548688
X-RAY DIFFRACTIONr_mcbond_other01.519391
X-RAY DIFFRACTIONr_mcangle_it1.646278768
X-RAY DIFFRACTIONr_scbond_it2.501330880
X-RAY DIFFRACTIONr_scangle_it3.6644.529888
Refine LS restraints NCS

Ens-ID: 1 / Number: 8177 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.080.05
2Btight positional0.090.05
3Ctight positional0.090.05
4Dtight positional0.090.05
5Etight positional0.090.05
6Ftight positional0.120.05
7Gtight positional0.090.05
8Htight positional0.090.05
9Itight positional0.090.05
10Jtight positional0.10.05
11Ktight positional0.10.05
12Ltight positional0.10.05
13Mtight positional0.10.05
14Ntight positional0.10.05
15Otight positional0.110.05
16Ptight positional0.10.05
1Atight thermal0.610.5
2Btight thermal0.570.5
3Ctight thermal0.570.5
4Dtight thermal0.570.5
5Etight thermal0.550.5
6Ftight thermal0.560.5
7Gtight thermal0.560.5
8Htight thermal0.620.5
9Itight thermal0.570.5
10Jtight thermal0.580.5
11Ktight thermal0.570.5
12Ltight thermal0.590.5
13Mtight thermal0.570.5
14Ntight thermal0.610.5
15Otight thermal0.550.5
16Ptight thermal0.650.5
LS refinement shellResolution: 2→2.024 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.271 467 -
Rwork0.215 8618 -
obs--43.51 %

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