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- PDB-5vtl: Structure of metacyclic invariant surface protein , Tb427.07.360,... -

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Basic information

Entry
Database: PDB / ID: 5vtl
TitleStructure of metacyclic invariant surface protein , Tb427.07.360, from Trypanosoma brucei.
ComponentsTb427.07.360- putative uncharacterized metacyclic invariant surface protein from Trypanosoma brucei
KeywordsUNKNOWN FUNCTION / Extended helical architecture / invariant surface protein
Function / homologyTrypanosoma glutamic acid/alanine-rich protein / Glutamic acid/alanine-rich protein of Trypanosoma / Tb427.07.360- putative uncharacterized metacyclic invariant surface protein from Trypanosoma brucei
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8231 Å
AuthorsRamswamy, R. / Workman, S.D. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: to be published
Title: Structure of Tb427.07.360, an insect stage antigen from Trypanosoma brucei.
Authors: Ramswamy, R. / Workman, S.D. / Boulanger, M.J.
History
DepositionMay 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tb427.07.360- putative uncharacterized metacyclic invariant surface protein from Trypanosoma brucei


Theoretical massNumber of molelcules
Total (without water)22,0881
Polymers22,0881
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.810, 79.500, 108.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tb427.07.360- putative uncharacterized metacyclic invariant surface protein from Trypanosoma brucei


Mass: 22087.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: Lister strain 427 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3F2YLN4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2014 / Details: Rh coated focusing mirror
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→44.72 Å / Num. obs: 136043 / % possible obs: 98.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.25 Å2 / Net I/σ(I): 20.8
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 6.9 % / Num. unique obs: 19605 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y44

2y44


Resolution: 1.8231→44.72 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.04
RfactorNum. reflection% reflection
Rfree0.2043 996 5.1 %
Rwork0.1691 --
obs0.171 136043 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.03 Å2 / Biso mean: 12.3 Å2 / Biso min: 2.2 Å2
Refinement stepCycle: final / Resolution: 1.8231→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 273 1819
Biso mean---18.02 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011565
X-RAY DIFFRACTIONf_angle_d1.1392111
X-RAY DIFFRACTIONf_chiral_restr0.054242
X-RAY DIFFRACTIONf_plane_restr0.005284
X-RAY DIFFRACTIONf_dihedral_angle_d12.952571
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8231-1.91920.26721300.18542526265694
1.9192-2.03940.23141620.16182541270397
2.0394-2.19690.18671210.15332604272598
2.1969-2.41790.18741310.15062629276098
2.4179-2.76770.19321310.16382692282399
2.7677-3.48660.21671590.180827052864100
3.4866-37.31830.19111620.17742849301199

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