[English] 日本語
Yorodumi
- PDB-2y44: Crystal structure of GARP from Trypanosoma congolense -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y44
TitleCrystal structure of GARP from Trypanosoma congolense
ComponentsGLUTAMIC ACID/ALANINE-RICH PROTEIN
KeywordsMEMBRANE PROTEIN / SURFACE PROTEIN
Function / homologyTrypanosoma glutamic acid/alanine-rich protein / Glutamic acid/alanine-rich protein of Trypanosoma / Ferritin - #80 / Ferritin / Up-down Bundle / Mainly Alpha / IODIDE ION / Alanine-rich surface protein / Glutamic acid/alanine-rich protein
Function and homology information
Biological speciesTRYPANOSOMA CONGOLENSE (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.65 Å
AuthorsLoveless, B.C. / Mason, J.W. / Sakurai, T. / Inoue, N. / Razavi, M. / Pearson, T.W. / Boulanger, M.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Characterization and Epitope Mapping of the Glutamic Acid/Alanine-Rich Protein from Trypanosoma Congolense: Defining Assembly on the Parasite Cell Surface.
Authors: Loveless, B.C. / Mason, J.W. / Sakurai, T. / Inoue, N. / Razavi, M. / Pearson, T.W. / Boulanger, M.J.
History
DepositionJan 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: GLUTAMIC ACID/ALANINE-RICH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9956
Polymers19,3951
Non-polymers6005
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.184, 37.795, 40.680
Angle α, β, γ (deg.)106.17, 111.75, 99.50
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein GLUTAMIC ACID/ALANINE-RICH PROTEIN / GARP


Mass: 19395.477 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 40-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CONGOLENSE (eukaryote) / Strain: IL3000 / Plasmid: PGEX-4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9U0E1, UniProt: Q07419*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGENE CLONED FROM A SPECIFIC STRAIN AND WITH THE KNOWN LEVEL OF POLYMORPHISM IN THIS FAMILY OF ...GENE CLONED FROM A SPECIFIC STRAIN AND WITH THE KNOWN LEVEL OF POLYMORPHISM IN THIS FAMILY OF GENES, THERE IS NO EXACT SEQUENCE PUBLISHED. HOWEVER, SEQUENCES FROM SEVERAL CLONES (SEVERAL PCR REACTIONS) INDICATE THAT DIFFERENCES IN SEQUENCE ARE SIMPLY ONE OF THE MANY POLYMORPHISMS. THUS THERE IS ONLY A "LOOSE" SEQUENCE REFERENCE CROSS-REFERENCE POSSIBLE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorDetails: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→34.62 Å / Num. obs: 20523 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 7.86 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.5 / % possible all: 89

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.65→34.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.171 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25085 1059 5.2 %RANDOM
Rwork0.19923 ---
obs0.20176 19462 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2--0 Å20.01 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 10 255 1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221364
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9731836
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84124.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10615248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5951513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02995
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4811.5914
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54421440
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6113450
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.5954.5396
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: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 93 -
Rwork0.334 1331 -
obs--88.5 %

+
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