[English] 日本語
Yorodumi
- PDB-3qb2: The Crystal Structure of Immunity Factor for SPN (IFS) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qb2
TitleThe Crystal Structure of Immunity Factor for SPN (IFS)
ComponentsImmunity factor for SPN
KeywordsHYDROLASE INHIBITOR / Glycohydrolase Inhibitor / Streptococcus pyogenes glycohydrolase toxin
Function / homologySerine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #520 / Immunity factor for SPN / IFS superfamily / Immunity factor for SPN / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / Immunity factor for SPN
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSmith, C.L. / Ellenberger, T.
CitationJournal: Structure / Year: 2011
Title: Structural Basis of Streptococcus pyogenes Immunity to Its NAD(+) Glycohydrolase Toxin.
Authors: Smith, C.L. / Ghosh, J. / Elam, J.S. / Pinkner, J.S. / Hultgren, S.J. / Caparon, M.G. / Ellenberger, T.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: Immunity factor for SPN
B: Immunity factor for SPN
C: Immunity factor for SPN
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,03710
Polymers89,4604
Non-polymers5766
Water2,792155
1
A: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6534
Polymers22,3651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,3651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,3651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,3651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Immunity factor for SPN
B: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1146
Polymers44,7302
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-66 kcal/mol
Surface area16370 Å2
MethodPISA
6
C: Immunity factor for SPN
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9224
Polymers44,7302
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-46 kcal/mol
Surface area17040 Å2
MethodPISA
7
A: Immunity factor for SPN
B: Immunity factor for SPN
hetero molecules

C: Immunity factor for SPN
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,03710
Polymers89,4604
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area10970 Å2
ΔGint-147 kcal/mol
Surface area30340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.032, 108.032, 147.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Immunity factor for SPN / SPN immunity factor


Mass: 22365.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: ifs / Production host: Escherichia coli (E. coli) / References: UniProt: Q2VJ58
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHOR STATES THAT THE C-TERMINAL 26 RESIDUES ARE MADE OF LINKER (FRSFL), MOUSE C-MYC (EQKLISEEDL), ...AUTHOR STATES THAT THE C-TERMINAL 26 RESIDUES ARE MADE OF LINKER (FRSFL), MOUSE C-MYC (EQKLISEEDL), LINKER (NSAVD) AND 6XHIS TAGS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6-2.0 ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97901, 0.97932, 0.99504
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 1, 2005
Details: Rosenbaum-Rock Si(111) sagitally focused monochromator
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979321
30.995041
ReflectionResolution: 2.5→46.8 Å / Num. obs: 34514 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.24 % / Rsym value: 0.069

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
REFMAC5.5.0070refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→46.78 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.862 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28986 1739 5 %RANDOM
Rwork0.25875 ---
all0.26042 66456 --
obs0.26042 32775 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 30 155 5085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225032
X-RAY DIFFRACTIONr_bond_other_d0.0010.023104
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.9686852
X-RAY DIFFRACTIONr_angle_other_deg0.87337595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0655647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23824.654217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.215750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0661515
X-RAY DIFFRACTIONr_chiral_restr0.0660.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
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_it0.5251.53242
X-RAY DIFFRACTIONr_mcbond_other0.0741.51310
X-RAY DIFFRACTIONr_mcangle_it1.03125094
X-RAY DIFFRACTIONr_scbond_it1.6931790
X-RAY DIFFRACTIONr_scangle_it2.6734.51758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 151 -
Rwork0.372 2407 -
obs--99.92 %

+
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