[English] 日本語
Yorodumi
- PDB-3trs: The crystal structure of aspergilloglutamic peptidase from Asperg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3trs
TitleThe crystal structure of aspergilloglutamic peptidase from Aspergillus niger
Components
  • Aspergillopepsin-2 heavy chain
  • Aspergillopepsin-2 light chain
KeywordsHYDROLASE / ASPERGILLOGLUTAMIC PEPTIDASE / GLUTAMIC PEPTIDASE / BETA SANDWICH STRUCTURE
Function / homology
Function and homology information


aspergillopepsin II / glutamic-type endopeptidase activity / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase G1 / Peptidase G1 / Peptidase G1 superfamily / Peptidase A4 family / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSasaki, H. / Kubota, K. / Lee, W.C. / Ohtsuka, J. / Kojima, M. / Takahashi, K. / Tanokura, M.
CitationJournal: J.Biochem. / Year: 2012
Title: The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis.
Authors: Sasaki, H. / Kubota, K. / Lee, W.C. / Ohtsuka, J. / Kojima, M. / Iwata, S. / Nakagawa, A. / Takahashi, K. / Tanokura, M.
History
DepositionSep 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspergillopepsin-2 light chain
B: Aspergillopepsin-2 heavy chain
C: Aspergillopepsin-2 light chain
D: Aspergillopepsin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7396
Polymers44,5834
Non-polymers1562
Water3,567198
1
A: Aspergillopepsin-2 light chain
B: Aspergillopepsin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3703
Polymers22,2912
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-25 kcal/mol
Surface area8430 Å2
MethodPISA
2
C: Aspergillopepsin-2 light chain
D: Aspergillopepsin-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3703
Polymers22,2912
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-26 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.692, 65.842, 77.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Aspergillopepsin-2 light chain / Aspergillopepsin II light chain


Mass: 3919.114 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: Var. macrosporus / References: UniProt: P24665, aspergillopepsin II
#2: Protein Aspergillopepsin-2 heavy chain / Aspergillopepsin II heavy chain


Mass: 18372.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: Var. macrosporus / References: UniProt: P24665, aspergillopepsin II
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 2.7
Details: 1.3M AMMONIUM SULFATE, 0.1M GLYCINE BUFFER (PH 2.7), 5% (V/V) DMSO, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37983 / % possible obs: 95.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.25
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.24 / % possible all: 85.5

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y43

1y43


Resolution: 1.6→38.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.296 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2010 5 %RANDOM
Rwork0.208 ---
obs0.21 37970 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 8 198 3223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9254232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5875404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56826.496137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94315420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022400
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8651.52008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62823232
X-RAY DIFFRACTIONr_scbond_it2.48331084
X-RAY DIFFRACTIONr_scangle_it3.9894.51000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 137 -
Rwork0.313 2460 -
obs--85.51 %

+
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