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- PDB-2qr5: Aeropyrum pernix acylaminoacyl peptidase, H367A mutant -

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Basic information

Entry
Database: PDB / ID: 2qr5
TitleAeropyrum pernix acylaminoacyl peptidase, H367A mutant
ComponentsAcylamino-acid-releasing enzymeAcylaminoacyl-peptidase
KeywordsHYDROLASE / acylaminoacyl peptidase / thermophilic enzyme / oxyanion binding site / catalytic activity
Function / homology
Function and homology information


acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Peptidase/esterase 'gauge' 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHarmat, V. / Pallo, A. / Kiss, A.L. / Polgar, L.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase
Authors: Kiss, A.L. / Pallo, A. / Naray-Szabo, G. / Harmat, V. / Polgar, L.
History
DepositionJul 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 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 1.4Aug 30, 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

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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


Theoretical massNumber of molelcules
Total (without water)126,0832
Polymers126,0832
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-18.8 kcal/mol
Surface area38440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.270, 105.040, 114.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUAA7 - 887 - 88
21VALVALGLUGLUBB7 - 887 - 88
32HISHISLEULEUAA90 - 10690 - 106
42HISHISLEULEUBB90 - 10690 - 106
53ALAALAVALVALAA108 - 109108 - 109
63ALAALAVALVALBB108 - 109108 - 109
74PROPROVALVALAA111 - 221111 - 221
84PROPROVALVALBB111 - 221111 - 221
95VALVALLEULEUAA223 - 233223 - 233
105VALVALLEULEUBB223 - 233223 - 233
116LEULEUVALVALAA235 - 309235 - 309
126LEULEUVALVALBB235 - 309235 - 309
137LEULEUPROPROAA311 - 323311 - 323
147LEULEUPROPROBB311 - 323311 - 323
158ASPASPARGARGAA325 - 327325 - 327
168ASPASPARGARGBB325 - 327325 - 327
179SERSERLEULEUAA329 - 365329 - 365
189SERSERLEULEUBB329 - 365329 - 365
1910PHEPHEALAALAAA371 - 430371 - 430
2010PHEPHEALAALABB371 - 430371 - 430
2111GLUGLUSERSERAA432 - 496432 - 496
2211GLUGLUSERSERBB432 - 496432 - 496
2312GLUGLULYSLYSAA498 - 566498 - 566
2412GLUGLULYSLYSBB498 - 566498 - 566
2513LEULEUARGARGAA568 - 579568 - 579
2613LEULEUARGARGBB568 - 579568 - 579
DetailsThe biological assembly is a dimer built up by chains A and B of the asymmetric unit.

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Components

#1: Protein Acylamino-acid-releasing enzyme / Acylaminoacyl-peptidase / E.C.3.4.19.1 / acylaminoacyl-peptidase / AARE / Acyl-peptide hydrolase / APH


Mass: 63041.480 Da / Num. of mol.: 2 / Mutation: H367A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.35
Details: 169 mM sodium acetate, 0.4 mM EDTA, 2% PEG 4000 0.51% beta-octyl-glucoside, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 20, 2006
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 58729 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Biso Wilson estimate: 38.14 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.5 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.61 / Num. unique all: 18581 / Rsym value: 0.467 / % possible all: 93.6

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Processing

Software
NameVersionClassification
bioteXdata collection
MOLREPphasing
REFMAC5.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VE6 (ONE MONOMER)

1ve6


Resolution: 2.2→19.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.619 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22225 2982 5.1 %RANDOM
Rwork0.17739 ---
all0.17959 55723 --
obs0.17959 55723 93.34 %-
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: 35.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8657 0 0 183 8840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.97512030
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95451158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3722.697356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.015151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2381581
X-RAY DIFFRACTIONr_chiral_restr0.0910.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026746
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.23726
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.26109
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2468
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.59225805
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45739125
X-RAY DIFFRACTIONr_scbond_it2.05223414
X-RAY DIFFRACTIONr_scangle_it3.06732901
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 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2220tight positional0.050.05
1919medium positional0.140.5
2220tight thermal0.260.5
1919medium thermal0.932
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 229 -
Rwork0.259 3921 -
obs--90.95 %
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)
10.78340.02460.01110.37170.0091.5107-0.02960.15450.0445-0.03210.00650.0012-0.0363-0.01490.023-0.09740.0132-0.0033-0.064-0.0041-0.04512.593781.7629-14.2593
20.8490.00050.0040.7707-0.16191.14310.0125-0.13910.02320.1015-0.0403-0.0227-0.0951-0.03340.0278-0.0505-0.02560.0001-0.1322-0.0257-0.05587.744688.161135.3097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 5816 - 581
2X-RAY DIFFRACTION2BB6 - 5816 - 581

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