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- PDB-1ryy: Acetobacter turbidans alpha-amino acid ester hydrolase Y206A mutant -

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Basic information

Entry
Database: PDB / ID: 1ryy
TitleAcetobacter turbidans alpha-amino acid ester hydrolase Y206A mutant
Componentsalpha-amino acid ester hydrolase
KeywordsHYDROLASE / alpha/beta hydrolase fold / jellyroll fold
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: 2.8 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.M. / Polderman-Tijmes, J.J. / Jekel, P.A. / Williams, C. / Wybenga, G. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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


Theoretical massNumber of molelcules
Total (without water)582,8438
Polymers582,8438
Non-polymers00
Water5,783321
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)291,4224
Polymers291,4224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-38 kcal/mol
Surface area82980 Å2
MethodPISA
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)291,4224
Polymers291,4224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-36 kcal/mol
Surface area82830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.649, 177.513, 169.967
Angle α, β, γ (deg.)90.00, 91.03, 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
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
251A
261B
271C
281D
291E
301F
311G
321H

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISASPASPAA50 - 6010 - 20
21HISHISASPASPBB50 - 6010 - 20
31HISHISASPASPCC50 - 6010 - 20
41HISHISASPASPDD50 - 6010 - 20
51HISHISASPASPEE50 - 6010 - 20
61HISHISASPASPFF50 - 6010 - 20
71HISHISASPASPGG50 - 6010 - 20
81HISHISASPASPHH50 - 6010 - 20
92GLNGLNLEULEUAA71 - 9031 - 50
102GLNGLNLEULEUBB71 - 9031 - 50
112GLNGLNLEULEUCC71 - 9031 - 50
122GLNGLNLEULEUDD71 - 9031 - 50
132GLNGLNLEULEUEE71 - 9031 - 50
142GLNGLNLEULEUFF71 - 9031 - 50
152GLNGLNLEULEUGG71 - 9031 - 50
162GLNGLNLEULEUHH71 - 9031 - 50
173THRTHRHISHISAA110 - 45570 - 415
183THRTHRHISHISBB110 - 45570 - 415
193THRTHRHISHISCC110 - 45570 - 415
203THRTHRHISHISDD110 - 45570 - 415
213THRTHRHISHISEE110 - 45570 - 415
223THRTHRHISHISFF110 - 45570 - 415
233THRTHRHISHISGG110 - 45570 - 415
243THRTHRHISHISHH110 - 45570 - 415
254TYRTYRLYSLYSAA470 - 666430 - 626
264TYRTYRLYSLYSBB470 - 666430 - 626
274TYRTYRLYSLYSCC470 - 666430 - 626
284TYRTYRLYSLYSDD470 - 666430 - 626
294TYRTYRLYSLYSEE470 - 666430 - 626
304TYRTYRLYSLYSFF470 - 666430 - 626
314TYRTYRLYSLYSGG470 - 666430 - 626
324TYRTYRLYSLYSHH470 - 666430 - 626

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Components

#1: Protein
alpha-amino acid ester hydrolase


Mass: 72855.375 Da / Num. of mol.: 8 / Fragment: Alpha-amino acid ester hydrolase / Mutation: Y206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter pasteurianus (bacteria) / Gene: aeha / Plasmid: pBADAtY206AmycHis / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8VRK8, alpha-amino-acid esterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium acetate, PEG 4000, ammonium acetate, 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: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2002
RadiationMonochromator: SI crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 134932 / Num. obs: 134932 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.066 / Net I/σ(I): 17.2
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 6.9 / Rsym value: 0.184 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.898 / SU B: 14.779 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.309 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS REFINEMENT EMPLOYED. The density for residues 66-70 in each of the monomers was not clear. Thus these residues have not been modelled.
RfactorNum. reflection% reflectionSelection details
Rfree0.23587 6623 5 %RANDOM
Rwork0.20972 ---
all0.21104 125204 --
obs0.21104 125204 99.45 %-
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: 19.549 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0.2 Å2
2--4.51 Å20 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38688 0 0 321 39009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02139936
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.92854528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.51854880
X-RAY DIFFRACTIONr_chiral_restr0.1220.25656
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0231776
X-RAY DIFFRACTIONr_nbd_refined0.1540.316941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.5506
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.365
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.55
Refine LS restraints NCS

Ens-ID: 1 / Number: 4559 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Dom-IDAuth asym-IDRms dev position (Å)
1A0.08
2B0.08
3C0.07
4D0.07
5E0.07
6F0.07
7G0.07
8H0.07
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 463
Rwork0.287 9034
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45820.072-0.04210.7418-0.21780.59820.02870.0747-0.0646-0.03540.0270.08350.0579-0.0388-0.05570.1353-0.0066-0.02530.0377-0.01050.1369-8.3098-15.315657.9637
20.6572-0.2130.29710.851-0.14740.72510.0071-0.14590.09770.08140.01210.1054-0.0449-0.1154-0.01930.1513-0.02790.05840.0364-0.01810.164-10.90511.78998.241
30.8183-0.0493-0.14250.6660.14870.95090.0688-0.0804-0.13270.05130.0152-0.14340.11630.2024-0.0840.17650.014-0.06350.02730.0130.185828.039-19.29590.454
40.58390.08110.13930.61180.20710.94620.01430.06670.2007-0.01550.0494-0.0638-0.14270.1803-0.06370.1434-0.07350.06390.05330.02090.212124.09422.54565.703
50.7242-0.0179-0.11931.0549-0.13670.6592-0.093-0.2517-0.01950.22640.15560.1917-0.0678-0.1894-0.06260.25750.06220.07950.64280.12950.217937.34257.90624.054
60.80880.0586-0.11530.9379-0.16840.7466-0.0133-0.0071-0.1376-0.11810.0850.15870.1698-0.3476-0.07170.1987-0.1125-0.02510.53730.09560.163939.07763.171-24.306
70.5223-0.08290.01370.592-0.34021.3929-0.0181-0.21060.13050.17350.0501-0.0685-0.1446-0.051-0.0320.20950.0246-0.0060.3352-0.050.17973.59984.8615.25
80.75310.0829-0.37460.7757-0.26811.0698-0.1622-0.1226-0.2328-0.11280.0369-0.09710.17430.04720.12530.2724-0.03730.07310.30240.08270.283774.2936.651-2.929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA50 - 66610 - 626
2X-RAY DIFFRACTION2BB50 - 66610 - 626
3X-RAY DIFFRACTION3CC50 - 66610 - 626
4X-RAY DIFFRACTION4DD50 - 66610 - 626
5X-RAY DIFFRACTION5EE50 - 66610 - 626
6X-RAY DIFFRACTION6FF50 - 66610 - 626
7X-RAY DIFFRACTION7GG50 - 66610 - 626
8X-RAY DIFFRACTION8HH50 - 66610 - 626

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