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- PDB-5kmx: Structure of Trypanosoma congolense Insect Stage Antigen -

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Basic information

Entry
Database: PDB / ID: 5kmx
TitleStructure of Trypanosoma congolense Insect Stage Antigen
Components(Putative uncharacterized protein TCIL3000_10_9440) x 2
KeywordsMEMBRANE PROTEIN / Bi-lobed architecture / surface protein / putative sensor
Function / homologyExtensin domain / Extensin-like region / structural constituent of cell wall / membrane => GO:0016020 / Uncharacterized protein TCIL3000_10_9440
Function and homology information
Biological speciesTrypanosoma congolense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å
Model detailsBi-lobed protein
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 27, 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 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein TCIL3000_10_9440
B: Putative uncharacterized protein TCIL3000_10_9440
C: Putative uncharacterized protein TCIL3000_10_9440
D: Putative uncharacterized protein TCIL3000_10_9440
U: Putative uncharacterized protein TCIL3000_10_9440
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,74315
Polymers105,7905
Non-polymers95310
Water1,22568
1
A: Putative uncharacterized protein TCIL3000_10_9440
U: Putative uncharacterized protein TCIL3000_10_9440
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8317
Polymers27,3552
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein TCIL3000_10_9440
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4294
Polymers26,1451
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein TCIL3000_10_9440
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3373
Polymers26,1451
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein TCIL3000_10_9440


Theoretical massNumber of molelcules
Total (without water)26,1451
Polymers26,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.810, 87.651, 98.891
Angle α, β, γ (deg.)90.000, 113.270, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by size exclusion chromatography.

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Components

#1: Protein
Putative uncharacterized protein TCIL3000_10_9440


Mass: 26145.184 Da / Num. of mol.: 4 / Fragment: residues 40-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Strain: IL3000 / Gene: TCIL3000_10_9440 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G0UXP9
#2: Protein/peptide Putative uncharacterized protein TCIL3000_10_9440


Mass: 1209.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Strain: IL3000 / Gene: TCIL3000_10_9440 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 20% PEG 3350 with 0.2 M (NH4)2SO4

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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 / Details: Rh coated flat, toroidal focusing
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→39.472 Å / Num. obs: 42706 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 64.65 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.8
Reflection shellResolution: 2.452→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.821 / % possible all: 98.34

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KLH

5klh


Resolution: 2.452→39.472 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.26
RfactorNum. reflection% reflection
Rfree0.2889 2140 5.01 %
Rwork0.2576 --
obs0.2592 42693 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.95 Å2 / Biso mean: 64.65 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.452→39.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 52 68 6340
Biso mean--72.31 51.86 -
Num. residues----778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036412
X-RAY DIFFRACTIONf_angle_d0.7638637
X-RAY DIFFRACTIONf_chiral_restr0.03911
X-RAY DIFFRACTIONf_plane_restr0.0041120
X-RAY DIFFRACTIONf_dihedral_angle_d13.2692393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.452-2.5090.35721370.34662696283398
2.509-2.57170.37891590.35062707286699
2.5717-2.64120.34761360.34932727286398
2.6412-2.71890.38991530.35742668282198
2.7189-2.80670.42471270.34012619274694
2.8067-2.9070.38031300.34362666279697
2.907-3.02330.33051390.31662726286599
3.0233-3.16090.3581460.31442735288199
3.1609-3.32740.3711490.29012715286499
3.3274-3.53580.36581440.272749289399
3.5358-3.80860.29391370.26122743288098
3.8086-4.19150.23881410.23392548268993
4.1915-4.79710.22451350.19512768290399
4.7971-6.04030.22431410.2152767290899
6.0403-39.47730.26991660.24762719288596

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