[English] 日本語
Yorodumi
- PDB-8ddp: Crystal structure of SRS57 from Toxoplasma gondii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ddp
TitleCrystal structure of SRS57 from Toxoplasma gondii
ComponentsSAG-related sequence SRS57
KeywordsMEMBRANE PROTEIN / Surface Antigen Glycoprotein / SAG / Related Sequences / SRS
Function / homologyProtozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / membrane / SAG-related sequence SRS57
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsRamaswamy, R. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structure of SRS29C from Toxoplasma gondii
Authors: Ramaswamy, R. / Boulanger, M.J.
History
DepositionJun 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: SAG-related sequence SRS57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3182
Polymers31,2261
Non-polymers921
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, eluted as a monomer in size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.130, 59.710, 101.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SAG-related sequence SRS57


Mass: 31226.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: SRS57, TGME49_308020 / Plasmid: pAcGP67b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A125YY85
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.59→43.48 Å / Num. obs: 40027 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.6
Reflection shellResolution: 1.59→1.62 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 1927

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZQ

1kzq


Resolution: 1.591→37.472 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 1950 4.88 %
Rwork0.1693 38011 -
obs0.1704 39961 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.27 Å2 / Biso mean: 22.9616 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: final / Resolution: 1.591→37.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 6 325 2513
Biso mean--29.82 31.5 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082268
X-RAY DIFFRACTIONf_angle_d1.2753079
X-RAY DIFFRACTIONf_chiral_restr0.051321
X-RAY DIFFRACTIONf_plane_restr0.007407
X-RAY DIFFRACTIONf_dihedral_angle_d13.793840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.591-1.63080.24471530.21992640
1.6308-1.67490.23471340.20822669
1.6749-1.72420.27391440.19482671
1.7242-1.77980.24781420.19052680
1.7798-1.84340.23461270.18092696
1.8434-1.91720.22551460.18362678
1.9172-2.00450.22691340.16832693
2.0045-2.11020.16941370.15812699
2.1102-2.24240.1891410.16442695
2.2424-2.41550.19141400.16072719
2.4155-2.65850.1921370.16892718
2.6585-3.0430.18961310.16282762
3.043-3.83330.16091300.16212787

+
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