[English] 日本語
Yorodumi
- PDB-5klh: Crystal Structure of Trypanosoma brucei Procyclic Specific Surfac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5klh
TitleCrystal Structure of Trypanosoma brucei Procyclic Specific Surface Antigen-2
ComponentsSurface glycoprotein
KeywordsMEMBRANE PROTEIN / Bi-lobed architecture / surface protein / putative sensor
Function / homologymembrane => GO:0016020 / Surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.646 Å
AuthorsRamaswamy, R. / Parker, M.L. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Protein Sci. / Year: 2016
Title: Structural characterization reveals a novel bilobed architecture for the ectodomains of insect stage expressed Trypanosoma brucei PSSA-2 and Trypanosoma congolense ISA.
Authors: Ramaswamy, R. / Goomeshi Nobary, S. / Eyford, B.A. / Pearson, T.W. / Boulanger, M.J.
History
DepositionJun 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface glycoprotein
B: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8823
Polymers50,7862
Non-polymers961
Water8,323462
1
A: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4892
Polymers25,3931
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Surface glycoprotein


Theoretical massNumber of molelcules
Total (without water)25,3931
Polymers25,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.820, 57.810, 61.240
Angle α, β, γ (deg.)73.550, 76.430, 89.980
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Surface glycoprotein


Mass: 25393.121 Da / Num. of mol.: 2 / Fragment: residues 40-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / References: UniProt: Q26806
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M (NH4)2SO4, 0.1 M Bis-tris pH 6.5, and 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.646→56.95 Å / Num. obs: 45400 / % possible obs: 92.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.3

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.646→47.122 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.36
RfactorNum. reflection% reflection
Rfree0.2141 2179 4.8 %
Rwork0.177 --
obs0.1788 45393 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.79 Å2 / Biso mean: 21.38 Å2 / Biso min: 6.62 Å2
Refinement stepCycle: final / Resolution: 1.646→47.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 5 462 3866
Biso mean--28.52 28.15 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073507
X-RAY DIFFRACTIONf_angle_d1.0684723
X-RAY DIFFRACTIONf_chiral_restr0.043491
X-RAY DIFFRACTIONf_plane_restr0.005624
X-RAY DIFFRACTIONf_dihedral_angle_d13.6681301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.646-1.68180.2871410.24412676281791
1.6818-1.72090.29381310.23162670280192
1.7209-1.7640.30821340.23752731286592
1.764-1.81170.25611280.22622674280292
1.8117-1.8650.26731580.19512718287692
1.865-1.92520.23661210.1962685280693
1.9252-1.9940.23371330.19182787292093
1.994-2.07380.24521350.18062650278593
2.0738-2.16820.21391430.18142705284893
2.1682-2.28250.23691330.18372771290493
2.2825-2.42550.21721200.18242710283093
2.4255-2.61280.241230.18292729285293
2.6128-2.87570.22031530.18342719287292
2.8757-3.29170.19761690.17312615278491
3.2917-4.14680.1841220.14572511263385
4.1468-47.14140.1591350.15062863299898

+
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