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- PDB-3o4i: Structure and Catalysis of Acylaminoacyl Peptidase -

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Basic information

Entry
Database: PDB / ID: 3o4i
TitleStructure and Catalysis of Acylaminoacyl Peptidase
ComponentsAcylamino-acid-releasing enzyme
KeywordsHYDROLASE / alpha/beta hydrolase fold / beta propeller / oligopeptidase / size selectivity
Function / homology
Function and homology information


acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Peptidase/esterase 'gauge' domain / : / Acylamino-acid-releasing enzyme-like, N-terminal domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Peptidase/esterase 'gauge' domain / : / Acylamino-acid-releasing enzyme-like, N-terminal domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHarmat, V. / Domokos, K. / Menyhard, D.K. / Pallo, A. / Szeltner, Z. / Szamosi, I. / Beke-Somfai, T. / Naray-Szabo, G. / Polgar, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Catalysis of Acylaminoacyl Peptidase: CLOSED AND OPEN SUBUNITS OF A DIMER OLIGOPEPTIDASE.
Authors: Harmat, V. / Domokos, K. / Menyhard, D.K. / Pallo, A. / Szeltner, Z. / Szamosi, I. / Beke-Somfai, T. / Naray-Szabo, G. / Polgar, L.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7179
Polymers126,1292
Non-polymers5887
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-33 kcal/mol
Surface area43190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.630, 209.890, 205.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLUGLU2AA6 - 176 - 17
211PROPROGLUGLU2BB6 - 176 - 17
121LEULEUALAALA2AA19 - 2119 - 21
221LEULEUALAALA2BB19 - 2119 - 21
131LEULEUPROPRO2AA322 - 323322 - 323
231LEULEUPROPRO2BB322 - 323322 - 323
141ASPASPLEULEU2AA325 - 326325 - 326
241ASPASPLEULEU2BB325 - 326325 - 326
151ARGARGGLUGLU2AA328 - 580328 - 580
251ARGARGGLUGLU2BB328 - 580328 - 580
112TYRTYRLEULEU2AA25 - 18725 - 187
212TYRTYRLEULEU2BB25 - 18725 - 187
122VALVALLEULEU4AA189 - 317189 - 317
222VALVALLEULEU4BB189 - 317189 - 317

NCS ensembles :
ID
1
2
DetailsThe biological assembly is homodimer. The asymmetric unit contains one dimer (chains A and B).

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Components

#1: Protein Acylamino-acid-releasing enzyme / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase


Mass: 63064.543 Da / Num. of mol.: 2 / Mutation: D524A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE_1547.1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 4.44 Å3/Da / Density % sol: 72.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 78mM sodium acetate, 0.44mM EDTA, 6.7mM dithiothreitol, 2.0% PEG 4000 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2008 / Details: mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 61532 / Num. obs: 61532 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.94 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 6.26 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4545 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hydrolase and propeller domains of PDB entry 2HU5.

2hu5


Resolution: 2.7→19.8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 23.051 / SU ML: 0.216 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25192 3091 5 %RANDOM
Rwork0.2071 ---
all0.20934 58407 --
obs0.20934 58407 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.197 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 37 335 8940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228807
X-RAY DIFFRACTIONr_bond_other_d0.0030.026011
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.97611956
X-RAY DIFFRACTIONr_angle_other_deg1.24314559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41451155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46422.564351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.576151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6631577
X-RAY DIFFRACTIONr_chiral_restr0.0970.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219981
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021850
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6371.55698
X-RAY DIFFRACTIONr_mcbond_other0.2671.52378
X-RAY DIFFRACTIONr_mcangle_it1.12329087
X-RAY DIFFRACTIONr_scbond_it1.93833109
X-RAY DIFFRACTIONr_scangle_it3.0654.52866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11584TIGHT POSITIONAL0.070.05
11704MEDIUM POSITIONAL0.130.5
11584TIGHT THERMAL0.130.5
11704MEDIUM THERMAL0.142
2942TIGHT POSITIONAL0.240.05
22663MEDIUM POSITIONAL0.330.5
2942TIGHT THERMAL0.790.5
22663MEDIUM THERMAL0.852
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 234 -
Rwork0.427 4216 -
obs--99.78 %
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)
11.20071.05360.23215.9298-0.59612.4795-0.13320.2368-0.1692-1.61420.23050.3010.2264-0.0654-0.09730.4757-0.0711-0.12460.2154-0.02760.221-39.6674-34.3629-19.084
21.54780.32-0.53785.2485-0.58422.9747-0.13840.2341-0.1073-0.8912-0.0314-0.51680.6460.2630.16980.39460.010.0940.28970.01910.1565-23.5639-4.6978-28.9728
32.7364-0.29420.23395.2858-0.1911.4433-0.02190.0613-0.2787-0.08780.0557-0.64520.19980.2325-0.03380.04550.0490.0560.18050.00420.2601-22.046-47.12115.5902
42.08310.10451.29492.61820.04732.98-0.0635-0.0225-0.0331-0.6209-0.04170.54890.0069-0.31520.10520.2179-0.0485-0.18950.18620.00610.1997-47.315217.6243-29.9567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 23
2X-RAY DIFFRACTION1A319 - 582
3X-RAY DIFFRACTION2B6 - 23
4X-RAY DIFFRACTION2B319 - 581
5X-RAY DIFFRACTION3A24 - 318
6X-RAY DIFFRACTION4B24 - 318

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