[English] 日本語
Yorodumi
- PDB-2uzj: Crystal structure of the mature streptococcal cysteine protease, mSpeB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uzj
TitleCrystal structure of the mature streptococcal cysteine protease, mSpeB
ComponentsSTREPTOPAIN
KeywordsHYDROLASE / PROTEINASE / PAPAIN FAMILY / CYSTEINE PROTEASE / DIMER / CLAN CA / EXOTOXIN / FAMILY 10 / PEPTIDASE
Function / homology
Function and homology information


streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / symbiont-mediated evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular region / cysteine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10, streptopain superfmaily / Peptidase C10 family / Streptopain (SpeB) / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-E64 / Streptopain / Streptopain
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOlsen, J.G. / Dagil, R. / Niclasen, L.M. / Soerensen, O.E. / Kragelund, B.B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of the Mature Streptococcal Cysteine Protease Exotoxin Mspeb in its Active Dimeric Form.
Authors: Olsen, J.G. / Dagil, R. / Niclasen, L.M. / Soerensen, O.E. / Kragelund, B.B.
History
DepositionSep 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STREPTOPAIN
B: STREPTOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9444
Polymers55,2232
Non-polymers7212
Water5,999333
1
A: STREPTOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9722
Polymers27,6121
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STREPTOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9722
Polymers27,6121
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.828, 60.888, 70.365
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein STREPTOPAIN / MATURE STREPTOCOCCAL PYROGENIC EXOTOXIN B / STREPTOCOCCAL CYSTEINE PROTEINASE / STREPTOCOCCUS ...MATURE STREPTOCOCCAL PYROGENIC EXOTOXIN B / STREPTOCOCCAL CYSTEINE PROTEINASE / STREPTOCOCCUS PEPTIDASE A / SPP / EXOTOXIN TYPE B / SPE B


Mass: 27611.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PROTEIN WAS PURIFIED FROM NATURAL SOURCE. / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / Strain: ALAB49
References: UniProt: Q5X9P3, UniProt: P0C0J0*PLUS, streptopain
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.52 %
Description: MOLECULAR REPLACEMENT SEARCH MODEL WAS 1DKI WITHOUT THE PROPEPTIDE
Crystal growDetails: 0.2 M (NH4)2SO4, 0.1 M NA-ACETATE, PH 4.0, 20 % PEG4000. PROTEIN KONCENTRATION WAS 0.07 MM (IN 20 MM NA-ACETATE, PH 5.0).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 2008 / Details: MIRRORS. MSC-CONFOCAL MAXFLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→21.48 Å / Num. obs: 63795 / % possible obs: 90.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.32
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 0.97 / % possible all: 55.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKI

1dki


Resolution: 1.55→21.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.602 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 234A-237A AND 234B-239B ARE ABSENT IN THE MODEL BECAUSE OF INSUFFICIENT ELECTRON DENSITY IN THESE REGIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3238 5.1 %RANDOM
Rwork0.181 ---
obs0.183 60554 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.01 Å2
2---0.05 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 50 333 4238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224007
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9375424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67624.949198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4815608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6331514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023172
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21999
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22774
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3251.52495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85523914
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.13431731
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4094.51510
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.444 122
Rwork0.367 2356

+
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