[English] 日本語
Yorodumi
- PDB-4d8b: High resolution structure of monomeric S. progenies SpeB reveals ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d8b
TitleHigh resolution structure of monomeric S. progenies SpeB reveals role of glycine-rich active site loop
ComponentsStreptopain
KeywordsHYDROLASE / papain fold / Cysteine Protease / Secreted
Function / homologyStreptopain (SpeB) / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / NITRATE ION / :
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.058 Å
AuthorsGonzalez, G.E. / Wolan, D.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Ultrahigh and High Resolution Structures and Mutational Analysis of Monomeric Streptococcus pyogenes SpeB Reveal a Functional Role for the Glycine-rich C-terminal Loop.
Authors: Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Aug 1, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptopain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7442
Polymers28,6821
Non-polymers621
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.994, 50.112, 41.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

21A-735-

HOH

-
Components

#1: Protein Streptopain


Mass: 28681.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC 10782 / Gene: HMPREF0841_0152, speB / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: E0PTS8, streptopain
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M Sodium Nitrate, 15% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.058→19.679 Å / Num. all: 111170 / Num. obs: 111095 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.058-1.084.80.5922.1183.6
1.08-1.14.50.5172.6189.5
1.1-1.124.20.4583.3194.5

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.058→19.679 Å / SU ML: 0.15 / σ(F): 0.56 / Phase error: 12.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1601 5358 5 %
Rwork0.1443 --
obs0.1451 107138 96.44 %
all-107464 -
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.89 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4328 Å20 Å2-0 Å2
2--1.3275 Å20 Å2
3----4.7603 Å2
Refinement stepCycle: LAST / Resolution: 1.058→19.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 4 449 2401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082012
X-RAY DIFFRACTIONf_angle_d1.3082734
X-RAY DIFFRACTIONf_dihedral_angle_d12.157715
X-RAY DIFFRACTIONf_chiral_restr0.071281
X-RAY DIFFRACTIONf_plane_restr0.007366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.058-1.07010.40181460.42442672X-RAY DIFFRACTION76
1.0701-1.08270.39551610.37192983X-RAY DIFFRACTION86
1.0827-1.09590.35881720.34743115X-RAY DIFFRACTION90
1.0959-1.10980.32871960.30913256X-RAY DIFFRACTION94
1.1098-1.12440.28461710.26453309X-RAY DIFFRACTION96
1.1244-1.13980.251820.2433429X-RAY DIFFRACTION98
1.1398-1.15610.23311680.20393424X-RAY DIFFRACTION99
1.1561-1.17330.16861860.17873429X-RAY DIFFRACTION99
1.1733-1.19160.18631920.16913497X-RAY DIFFRACTION100
1.1916-1.21120.15141810.14893453X-RAY DIFFRACTION100
1.2112-1.23210.14532000.13563474X-RAY DIFFRACTION100
1.2321-1.25450.14241850.12653465X-RAY DIFFRACTION100
1.2545-1.27860.13171690.1213518X-RAY DIFFRACTION100
1.2786-1.30470.141750.11743477X-RAY DIFFRACTION100
1.3047-1.3330.13551860.10963475X-RAY DIFFRACTION100
1.333-1.3640.15441820.10673506X-RAY DIFFRACTION100
1.364-1.39810.13351680.10273506X-RAY DIFFRACTION100
1.3981-1.43590.14391990.10433467X-RAY DIFFRACTION100
1.4359-1.47820.12231760.10193516X-RAY DIFFRACTION100
1.4782-1.52590.13661640.10993508X-RAY DIFFRACTION100
1.5259-1.58040.12811680.11233504X-RAY DIFFRACTION100
1.5804-1.64360.13411700.11223525X-RAY DIFFRACTION100
1.6436-1.71840.13451970.11533539X-RAY DIFFRACTION100
1.7184-1.80890.13071890.11583515X-RAY DIFFRACTION100
1.8089-1.92220.15921870.12753253X-RAY DIFFRACTION92
1.9222-2.07040.15272000.13183509X-RAY DIFFRACTION100
2.0704-2.27850.15251690.13273595X-RAY DIFFRACTION100
2.2785-2.60760.13961880.13943587X-RAY DIFFRACTION100
2.6076-3.28280.15261390.14772744X-RAY DIFFRACTION75
3.2828-19.68210.17281920.1683530X-RAY DIFFRACTION93

+
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