[English] 日本語
Yorodumi
- PDB-3muo: APPEP_PEPCLOSE+PP closed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3muo
TitleAPPEP_PEPCLOSE+PP closed state
ComponentsProlyl endopeptidase
KeywordsHydrolase/Hydrolase Inhibitor / PROLYL ENDOPEPTIDASE / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / : / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller ...Prolyl oligopeptidase, N-terminal domain / : / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / 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-PRO-PROLINAL / sucrose / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL / prolyl oligopeptidase
Similarity search - Component
Biological speciesAeromonas punctata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChiu, T.K.
CitationJournal: TO BE PUBLISHED
Title: Route of Substrate Entry in Prolyl Endopeptidase
Authors: Chiu, T.K. / Li, M.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,94811
Polymers77,2811
Non-polymers1,66810
Water10,737596
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.770, 107.770, 147.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Details1

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Prolyl endopeptidase


Mass: 77280.820 Da / Num. of mol.: 1 / Mutation: R86W, E87W, D245Q, K379Y, H380W, 381W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas punctata (bacteria) / Gene: PROLYL ENDOPEPTIDASE / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9X6R4
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 605 molecules

#3: Chemical ChemComp-ZPR / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL / Z-PRO-PROLINAL


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 330.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N2O4 / References: Z-PRO-PROLINAL
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsAUTHORS STATE THAT THESE ARE NOT MUTATIONS, BUT ERROR IN DNA SEQUENCING OF THE ORIGINAL DEPOSITED ...AUTHORS STATE THAT THESE ARE NOT MUTATIONS, BUT ERROR IN DNA SEQUENCING OF THE ORIGINAL DEPOSITED FILE. THEY CONFIRMED THIS WITH DNA SEQUENCING

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growpH: 7.5
Details: 8MG/ML PROTEIN IN 20MM HEPES (PH7.5), 100MM NACL, 5% W/V GLYCEROL, AND 1MM EDTA. EQUAL VOLUME OF PROTEIN AND PRECIPITANT (1.5M AMSO4, 100MM TRIS (PH 8.5) AND 12% W/V GLYCEROL) WERE ...Details: 8MG/ML PROTEIN IN 20MM HEPES (PH7.5), 100MM NACL, 5% W/V GLYCEROL, AND 1MM EDTA. EQUAL VOLUME OF PROTEIN AND PRECIPITANT (1.5M AMSO4, 100MM TRIS (PH 8.5) AND 12% W/V GLYCEROL) WERE EQUILIBRATED BY VAPOR DIFFUSION AT 14C. CRYOSOLUTION IS 2.2M AMSO4, 30% W/V SUCROSE, 12% W/V GLYCEROL AND 100MM TRIS (PH 8.5). CRYSTALS WERE SOAKED WITH 10MM OF THE INHIBITOR ZPR IN CRYOSOLUTION.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDetector: CCD / Date: Oct 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 73036 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.126 / Net I/σ(I): 17.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10 % / Mean I/σ(I) obs: 8.1 / Rsym value: 0.468 / % possible all: 100

-
Processing

Software
NameVersionClassification
EPMRphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IUJ

3iuj


Resolution: 1.95→36.28 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2848545.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3647 5 %RANDOM
Rwork0.16 ---
obs0.16 72517 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6933 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.95→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 101 596 6104
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.581.5
X-RAY DIFFRACTIONc_mcangle_it3.262
X-RAY DIFFRACTIONc_scbond_it4.312
X-RAY DIFFRACTIONc_scangle_it6.122.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.195 337 4.7 %
Rwork0.165 6808 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_spp.paramprotein_spp.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4zppoh.paramzppoh.top
X-RAY DIFFRACTION5sucrose.paramsucrose.top

+
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