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- PDB-4re6: Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor -

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Basic information

Entry
Database: PDB / ID: 4re6
TitleAcylaminoacyl peptidase complexed with a chloromethylketone inhibitor
ComponentsAcylamino-acid-releasing enzymeAcylaminoacyl-peptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-propeller / alpha-beta-hydrolase fold / chloromethyl-ketone inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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
Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) / Chem-Y3A / Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsMenyhard, D.K. / Orgovan, Z. / Szeltner, Z. / Szamosi, I. / Harmat, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality.
Authors: Menyhard, D.K. / Orgovan, Z. / Szeltner, Z. / Szamosi, I. / Harmat, V.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn / struct_site
Item: _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_dist_value ..._reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,54312
Polymers252,4344
Non-polymers1,1098
Water12,142674
1
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8077
Polymers126,2172
Non-polymers5905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-56 kcal/mol
Surface area40480 Å2
MethodPISA
2
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7365
Polymers126,2172
Non-polymers5193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-40 kcal/mol
Surface area40690 Å2
MethodPISA
3
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules

C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,54312
Polymers252,4344
Non-polymers1,1098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area6890 Å2
ΔGint-101 kcal/mol
Surface area80350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.580, 97.300, 99.160
Angle α, β, γ (deg.)105.15, 103.96, 100.26
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA6 - 5796 - 579
21PROPROBB6 - 5796 - 579
12METMETAA5 - 5815 - 581
22METMETCC5 - 5815 - 581
13METMETAA5 - 5815 - 581
23METMETDD5 - 5815 - 581
14PROPROBB6 - 5796 - 579
24PROPROCC6 - 5796 - 579
15PROPROBB6 - 5796 - 579
25PROPRODD6 - 5796 - 579
16METMETCC5 - 5815 - 581
26METMETDD5 - 5815 - 581

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 63108.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: APE_1547.1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Chemical ChemComp-Y3A / N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide / Z-Gly-Gly-Phe-Chloromethyl ketone (bound form)


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 447.912 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26ClN3O5
Details: The chlorormethyl ketone inhibitor linked to the protein through two covalent bonds with the active site serine and histidine
References: Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM)
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 78 mM sodium acetate buffer, 2.2% w/v PEG Mw4000, 5.2 mM dithiothreitol, 0.34 mM EDTA. Protein crystals were soaked in the inhibitor solution., pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2011 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 68281 / Num. obs: 68281 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.18 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
11.4-200.02239.03179.2
8.06-11.40.02336.15197.8
6.58-8.060.03726.03197.2
5.7-6.580.04221.87197.5
5.1-5.70.03923.35197.6
4.66-5.10.03525.11197.3
4.31-4.660.03525.23197.5
4.03-4.310.04121.83197
3.8-4.030.05420.52180.1
3.61-3.80.05919.18182.6
3.44-3.610.07214.46192.2
3.29-3.440.08512.03193.7
3.16-3.290.1079.82196.9
3.05-3.160.1347.78196.9
2.94-3.050.1716.23196.6
2.85-2.940.2195196.6
2.77-2.850.2724.04190.4
2.69-2.770.3872.9171.6
2.62-2.690.3183.5157.9
2.55-2.620.5052.16151.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3O4H

3o4h


Resolution: 2.55→19.85 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.861 / SU B: 23.075 / SU ML: 0.256 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25963 3441 5 %RANDOM, IMPORTED FROM ISOSTRUCTURAL DATA SET OF PDB ENTRY 3O4H.
Rwork0.21152 ---
obs0.21398 64833 86.52 %-
all-64833 --
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: 33.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20.42 Å20.11 Å2
2--0.63 Å20.14 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17267 0 49 674 17990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01917786
X-RAY DIFFRACTIONr_bond_other_d0.0070.0216844
X-RAY DIFFRACTIONr_angle_refined_deg1.471.97724181
X-RAY DIFFRACTIONr_angle_other_deg1.294338682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84452335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25122.51725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06152787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.54815163
X-RAY DIFFRACTIONr_chiral_restr0.0760.22704
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120342
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024003
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_it1.8812.399270
X-RAY DIFFRACTIONr_mcbond_other1.8812.399270
X-RAY DIFFRACTIONr_mcangle_it3.0123.58211584
X-RAY DIFFRACTIONr_mcangle_other2.9693.54411609
X-RAY DIFFRACTIONr_scbond_it2.2262.5638516
X-RAY DIFFRACTIONr_scbond_other2.1842.5348587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4583.72112674
X-RAY DIFFRACTIONr_long_range_B_refined5.19218.96919574
X-RAY DIFFRACTIONr_long_range_B_other5.15118.91819480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A312120.14
12B312120.14
21A353080.06
22C353080.06
31A312900.14
32D312900.14
41B313080.14
42C313080.14
51B333460.08
52D333460.08
61C311720.14
62D311720.14
LS refinement shellResolution: 2.55→2.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 126 -
Rwork0.285 2782 -
obs--50.99 %
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)
10.53380.18380.21220.84160.06640.7022-0.0466-0.03530.0572-0.052-0.00640.0429-0.0402-0.08820.0530.00970.0087-0.00450.065-0.0090.011-14.2054-20.2746-1.2164
20.37880.31730.36240.87010.06090.6759-0.01850.1309-0.0227-0.05350.06270.0682-0.00030.1382-0.04420.02320.00960.02610.10440.00950.061216.270219.238612.2314
30.74520.11940.08010.9372-0.18430.67430.03150.0708-0.03530.0646-0.0323-0.1117-0.03910.13020.00080.023-0.00490.00410.0457-0.010.0272-7.927338.0016-36.2516
40.82480.32140.29360.82580.15360.6143-0.0256-0.046-0.02180.03380.0558-0.02010.0465-0.0651-0.03020.06120.01470.03240.03880.00820.0253-39.5429-0.9279-49.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 581
2X-RAY DIFFRACTION2B6 - 580
3X-RAY DIFFRACTION3C5 - 581
4X-RAY DIFFRACTION4D5 - 581

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