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- PDB-4re5: Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor -

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Basic information

Entry
Database: PDB / ID: 4re5
TitleAcylaminoacyl peptidase complexed with a chloromethylketone inhibitor
ComponentsAcylamino-acid-releasing enzyme
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 / : / 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
Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) / ACETATE ION / Chem-Y3A / Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 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 / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_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
Revision 1.4Nov 6, 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: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,5629
Polymers126,2172
Non-polymers1,3457
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-58 kcal/mol
Surface area38200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.813, 104.430, 170.080
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 8 - 581 / Label seq-ID: 8 - 581

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is dimer consisting of chains A and B of the asymmetric unit.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 63108.551 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 669 molecules

#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 78 mM sodium acetate buffer, 2.4% w/v PEG Mw4000, 6.7mM dithiothreitol and 0.44 mM EDTA. The protein was co-crystallized with the inhibitor., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2010 / Details: mirrors (Blue)
RadiationMonochromator: Rigaku confocal Blue optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 90022 / Num. obs: 90022 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Biso Wilson estimate: 32.79 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.58
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6591 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2HU5

2hu5


Resolution: 1.9→19.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.984 / SU ML: 0.117 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 4499 5 %RANDOM, imported from isostructural data set of pdb entry 2HU5
Rwork0.17695 ---
all0.17902 85520 --
obs0.17902 85520 99.66 %-
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: 35.253 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---1.37 Å2-0 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8591 0 69 662 9322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198968
X-RAY DIFFRACTIONr_bond_other_d0.0060.028525
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9812208
X-RAY DIFFRACTIONr_angle_other_deg1.14319581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30351186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58122.568366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.426151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9331581
X-RAY DIFFRACTIONr_chiral_restr0.1010.21363
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110270
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022029
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_it1.8761.6454649
X-RAY DIFFRACTIONr_mcbond_other1.8761.6444648
X-RAY DIFFRACTIONr_mcangle_it2.7352.4535813
X-RAY DIFFRACTIONr_mcangle_other2.7352.4535814
X-RAY DIFFRACTIONr_scbond_it2.681.8914319
X-RAY DIFFRACTIONr_scbond_other2.6791.8914320
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9942.746377
X-RAY DIFFRACTIONr_long_range_B_refined7.08914.38210400
X-RAY DIFFRACTIONr_long_range_B_other7.08914.38310401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 34440 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 315 -
Rwork0.294 6271 -
obs-6271 99.88 %
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)
10.2618-0.11190.08480.8170.09090.1332-0.00190.04730.04050.0061-0.08310.1041-0.09140.0530.0850.1536-0.0056-0.04330.13740.00350.0829-6.302540.6544-19.5604
20.5075-0.85480.22222.8145-0.43340.11210.23570.0141-0.27950.0954-0.08830.7170.0830.0463-0.14730.2882-0.0077-0.08240.1156-0.08610.3182-21.0158-31.2765-22.2622
30.16840.0340.14450.65080.08290.16170.07890.0743-0.05190.0626-0.05570.0120.02050.057-0.02330.12350.0076-0.03640.1658-0.03330.10731.16713.6125-17.1942
40.07540.36890.01262.66920.01380.01780.03450.0170.0898-0.1342-0.03370.79420.01580.0521-0.00080.09090.0486-0.11430.1673-0.09030.3667-24.7643-4.7001-30.5172
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 320
2X-RAY DIFFRACTION2B23 - 320
3X-RAY DIFFRACTION3A8 - 22
4X-RAY DIFFRACTION3A321 - 581
5X-RAY DIFFRACTION4B8 - 22
6X-RAY DIFFRACTION4B321 - 581

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