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- PDB-5x6n: Structure of P. Knowlesi DBL Domain Capable of binding Human Duff... -

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Basic information

Entry
Database: PDB / ID: 5x6n
TitleStructure of P. Knowlesi DBL Domain Capable of binding Human Duffy Antigen
ComponentsDuffy binding protein
KeywordsCELL INVASION / RECEPTOR / DUFFY ANTIGEN / DBL DOMAIN / P.KNOWLESI / P.VIVAX
Function / homology
Function and homology information


: / membrane => GO:0016020 / host cell surface receptor binding
Similarity search - Function
Duffy-antigen binding, C-terminal / Duffy-antigen binding, N-terminal / Duffy-antigen binding protein / Duffy binding protein N terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Erythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding domain / Duffy-binding-like domain ...Duffy-antigen binding, C-terminal / Duffy-antigen binding, N-terminal / Duffy-antigen binding protein / Duffy binding protein N terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Erythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding domain / Duffy-binding-like domain / PFEMP1 DBL domain / 5 helical Cullin repeat like / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Duffy binding protein / Duffy receptor alpha form
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsSingh, S.K. / Hora, R. / Belrhali, H. / Chitnis, C. / Sharma, A.
CitationJournal: Nature / Year: 2006
Title: Structural basis for Duffy recognition by the malaria parasite Duffy-binding-like domain
Authors: Singh, S.K. / Hora, R. / Belrhali, H. / Chitnis, C.E. / Sharma, A.
History
DepositionFeb 22, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 8, 2017ID: 2C6J
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Duffy binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3904
Polymers39,9061
Non-polymers4843
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-13 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 60.570, 241.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Duffy binding protein / Duffy receptor


Mass: 39905.699 Da / Num. of mol.: 1 / Fragment: UNP residues 200-536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Gene: dbp alpha / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: L0SQ42, UniProt: P22545*PLUS
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 12% PEG 10K, 0.1M AMMONIUM SULFATE, 0.5% BETA-OCTYL GLUCOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3→19.581 Å / Num. obs: 9599 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 35.14
Reflection shellResolution: 3→3.34 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→19.581 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.2912 446 4.99 %
Rwork0.2458 --
obs0.248 8934 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→19.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 30 12 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062313
X-RAY DIFFRACTIONf_angle_d1.0563089
X-RAY DIFFRACTIONf_dihedral_angle_d14.514899
X-RAY DIFFRACTIONf_chiral_restr0.036311
X-RAY DIFFRACTIONf_plane_restr0.004388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.43220.37191310.31542491X-RAY DIFFRACTION84
3.4322-4.31660.28131500.24662866X-RAY DIFFRACTION95
4.3166-19.58170.2761650.22873131X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 59.0973 Å / Origin y: 26.6362 Å / Origin z: 98.4084 Å
111213212223313233
T0.5333 Å20.0365 Å2-0.1132 Å2-0.6483 Å2-0.115 Å2--0.6827 Å2
L0.5819 °20.6251 °21.2679 °2-1.9398 °22.6732 °2--5.2864 °2
S0.1627 Å °0.2456 Å °-0.2335 Å °0.4664 Å °0.3436 Å °-0.4546 Å °0.5495 Å °0.8136 Å °-0.3901 Å °
Refinement TLS groupSelection details: all

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