[English] 日本語
Yorodumi
- PDB-3o4j: Structure and Catalysis of Acylaminoacyl Peptidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o4j
TitleStructure and Catalysis of Acylaminoacyl Peptidase
ComponentsAcylamino-acid-releasing enzymeAcylaminoacyl-peptidase
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 / 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: 2.5 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 6, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)252,98512
Polymers252,4304
Non-polymers5548
Water9,638535
1
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4016
Polymers126,2152
Non-polymers1864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area41430 Å2
MethodPISA
2
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5846
Polymers126,2152
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area41430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.270, 227.524, 110.684
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23C
14B
24D

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
111PROPROALAALA3AA6 - 216 - 21
211PROPROALAALA3CC6 - 216 - 21
121LEULEUGLUGLU3AA322 - 580322 - 580
221LEULEUGLUGLU3CC322 - 580322 - 580
112PROPROALAALA3BB6 - 216 - 21
212PROPROALAALA3DD6 - 216 - 21
122LEULEUSERSER3BB322 - 340322 - 340
222LEULEUSERSER3DD322 - 340322 - 340
132ASPASPGLUGLU3BB342 - 580342 - 580
232ASPASPGLUGLU3DD342 - 580342 - 580
113TYRTYRLEULEU3AA25 - 18725 - 187
213TYRTYRLEULEU3CC25 - 18725 - 187
123VALVALLEULEU4AA189 - 317189 - 317
223VALVALLEULEU4CC189 - 317189 - 317
114TYRTYRLEULEU3BB25 - 31725 - 317
214TYRTYRLEULEU3DD25 - 31725 - 317

NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly is homodimer. One dimer consists of chains A and B, and the other dimer consists of chains C and D.

-
Components

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


Mass: 63107.566 Da / Num. of mol.: 4 / Mutation: D524N
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 170mM sodium acetate, 0.4mM EDTA, 10% dimethyl sulphoxide, 2.5% PEG 4000 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 12, 2009 / Details: mirror
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 149375 / Num. obs: 149375 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.43
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.48 / Num. unique all: 16732 / % possible all: 98.8

-
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: 2.5→29.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.687 / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23589 7519 5 %RANDOM
Rwork0.19914 ---
all0.20099 141856 --
obs0.20099 141856 96.89 %-
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: 35.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.02 Å2
2--0.11 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17452 0 33 535 18020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02217965
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212417
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.97424378
X-RAY DIFFRACTIONr_angle_other_deg1.12330039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24552330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22922.487760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.887152874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.25415174
X-RAY DIFFRACTIONr_chiral_restr0.0970.22705
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120338
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023816
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_it0.6421.511445
X-RAY DIFFRACTIONr_mcbond_other0.3541.54770
X-RAY DIFFRACTIONr_mcangle_it1.065218333
X-RAY DIFFRACTIONr_scbond_it1.85536520
X-RAY DIFFRACTIONr_scangle_it2.8184.56033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1606TIGHT POSITIONAL0.040.05
1A1965LOOSE POSITIONAL0.15
1A1606TIGHT THERMAL0.160.5
1A1965LOOSE THERMAL0.1610
2B1581TIGHT POSITIONAL0.050.05
2B1878LOOSE POSITIONAL0.135
2B1581TIGHT THERMAL0.160.5
2B1878LOOSE THERMAL0.1610
3A939TIGHT POSITIONAL0.080.05
3A1667MEDIUM POSITIONAL0.120.5
3A1062LOOSE POSITIONAL0.225
3A939TIGHT THERMAL0.670.5
3A1667MEDIUM THERMAL0.82
3A1062LOOSE THERMAL0.9610
4B1700TIGHT POSITIONAL0.040.05
4B1984LOOSE POSITIONAL0.085
4B1700TIGHT THERMAL0.160.5
4B1984LOOSE THERMAL0.1510
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 519 -
Rwork0.345 10589 -
obs--98.01 %
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)
11.48750.3444-0.61581.8152-0.12092.0207-0.1320.12560.0044-0.35210.16810.17670.0804-0.3727-0.03610.2268-0.2145-0.03060.2845-0.02080.1339-38.7161-12.1574-39.166
21.67480.9444-0.68652.14680.67912.685-0.17580.19980.0472-0.23230.19610.03160.022-0.0717-0.02030.0326-0.0191-0.01690.1068-0.00120.1005-19.999511.4554-21.6441
31.405-0.1534-0.0751.7691-0.1531.15580.07510.0482-0.0637-0.2044-0.061-0.05740.27170.1542-0.01410.11570.0830.01150.1457-0.00390.077533.86840.4366-37.2396
41.52890.50730.81463.0698-1.11582.7182-0.11910.0415-0.2188-0.28510.21590.37030.0191-0.1221-0.09680.11510.0930.01180.17990.02350.284217.0992-22.557-17.1486
51.32180.5079-0.61681.9723-0.22332.2087-0.25070.1211-0.2325-0.50580.1453-0.30950.68780.13160.10540.4546-0.13620.14640.2243-0.12660.2621-23.5215-35.5086-38.2769
61.7-0.54290.44742.6938-0.17851.46310.05080.07760.0004-0.3148-0.02760.338-0.1494-0.2214-0.02320.06550.0569-0.04830.1223-0.02010.1407-40.71631.3309-5.502
71.40610.13350.34551.1378-0.26571.6703-0.01410.04440.1014-0.1434-0.02210.0291-0.0774-0.03350.03630.02770.0146-0.01090.08660.00850.08319.387324.248-34.3941
81.7032-0.7392-0.57822.92930.44371.76560.13030.105-0.0039-0.09710.0145-0.0790.05370.0631-0.14470.16760.1143-0.01950.12940.07050.180339.2274-42.9765-4.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 23
2X-RAY DIFFRACTION1A319 - 581
3X-RAY DIFFRACTION2B6 - 23
4X-RAY DIFFRACTION2B319 - 581
5X-RAY DIFFRACTION3C4 - 23
6X-RAY DIFFRACTION3C319 - 582
7X-RAY DIFFRACTION4D6 - 23
8X-RAY DIFFRACTION4D319 - 581
9X-RAY DIFFRACTION5A24 - 318
10X-RAY DIFFRACTION6B24 - 318
11X-RAY DIFFRACTION7C24 - 318
12X-RAY DIFFRACTION8D24 - 318

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more