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- PDB-4e40: The haptoglobin-hemoglobin receptor of Trypanosoma congolense -

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Basic information

Entry
Database: PDB / ID: 4.0E+40
TitleThe haptoglobin-hemoglobin receptor of Trypanosoma congolense
ComponentsPutative uncharacterized protein
KeywordsTRANSPORT PROTEIN / haptoglobin-hemoglobin receptor / helical bundle / receptor / cell surface
Function / homology: / Haptoglobin-hemoglobin receptor / Ferritin - #80 / Ferritin / Up-down Bundle / Mainly Alpha / metal ion binding / membrane / Uncharacterized protein
Function and homology information
Biological speciesTrypanosoma congolense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsHiggins, M.K. / Tkachenko, O. / Brown, A. / Reed, J. / Carrington, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of the trypanosome haptoglobin-hemoglobin receptor and implications for nutrient uptake and innate immunity.
Authors: Higgins, M.K. / Tkachenko, O. / Brown, A. / Reed, J. / Raper, J. / Carrington, M.
History
DepositionMar 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,8511
Polymers26,8511
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)53,7022
Polymers53,7022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2930 Å2
ΔGint-7 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.530, 104.530, 113.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 26850.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Strain: IL3000 / Gene: TCIL3000_10_2930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UVW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPLEASE SEE PRIMARY CITATION FOR THE DETAILED EXPLANATION OF THE DISCREPANCIES BETWEEN THE UNIPROT ...PLEASE SEE PRIMARY CITATION FOR THE DETAILED EXPLANATION OF THE DISCREPANCIES BETWEEN THE UNIPROT ENTRY AND PROVIDED SEQUENCE

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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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% PEG 12,000, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: single bounce / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.6→90.53 Å / Num. all: 46112 / Num. obs: 46112 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→90.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.984 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22332 2455 5.1 %RANDOM
Rwork0.20588 ---
all0.20677 46112 --
obs0.20677 46112 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→90.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 0 263 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191905
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9722576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1265258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30126.51286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2631511
X-RAY DIFFRACTIONr_chiral_restr0.1250.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021417
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 165 -
Rwork0.266 3088 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 27.799 Å / Origin y: -17.1458 Å / Origin z: -2.7568 Å
111213212223313233
T0.0959 Å2-0.0317 Å2-0.0016 Å2-0.0197 Å2-0.0116 Å2--0.0233 Å2
L0.1798 °20.0694 °20.1348 °2-0.9604 °20.56 °2--0.3815 °2
S0.017 Å °-0.0088 Å °0.0095 Å °-0.0119 Å °-0.0429 Å °0.0179 Å °-0.0034 Å °-0.0322 Å °0.026 Å °

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