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- PDB-4yfs: Structure of the synthetic Duffy Binding Protein (DBP) antigen DE... -

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Basic information

Entry
Database: PDB / ID: 4yfs
TitleStructure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for malaria vaccine design
ComponentsDuffy receptor
KeywordsErythrocyte binding protein / Duffy binding like domain / invasion / malaria / vaccine
Function / homology
Function and homology information


host cell surface receptor binding / identical protein binding / membrane
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 / 5 helical Cullin repeat like ...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 / 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
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, E. / Tolia, N.H.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI064478 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007171 United States
Edward Mallinckrodt Jr. Foundation United States
Burroughs Wellcome Fund United States
Schlesinger Graduate Fellowship United States
CitationJournal: Plos Negl Trop Dis / Year: 2015
Title: Structural Analysis of the Synthetic Duffy Binding Protein (DBP) Antigen DEKnull Relevant for Plasmodium vivax Malaria Vaccine Design.
Authors: Chen, E. / Salinas, N.D. / Ntumngia, F.B. / Adams, J.H. / Tolia, N.H.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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

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Assembly

Deposited unit
A: Duffy receptor


Theoretical massNumber of molelcules
Total (without water)38,2581
Polymers38,2581
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.630, 37.350, 78.200
Angle α, β, γ (deg.)90.00, 108.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Duffy receptor / Erythrocyte-binding protein


Mass: 38257.879 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 198-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVDR / Production host: Escherichia coli (E. coli) / References: UniProt: P22290
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M di-sodium tartrate, 20% PEG 3350, and microseeded into 0.2 M lithium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000087 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000087 Å / Relative weight: 1
ReflectionResolution: 2.1→26.537 Å / Num. obs: 17538 / % possible obs: 96.7 % / Redundancy: 2.93 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.51
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.11 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRC

3rrc


Resolution: 2.1→26.536 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1764 10.06 %Random selection
Rwork0.2177 ---
obs0.222 17535 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→26.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 128 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042448
X-RAY DIFFRACTIONf_angle_d0.7493289
X-RAY DIFFRACTIONf_dihedral_angle_d13.989933
X-RAY DIFFRACTIONf_chiral_restr0.029348
X-RAY DIFFRACTIONf_plane_restr0.003413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15690.32641340.2631206X-RAY DIFFRACTION97
2.1569-2.22030.28341430.23791218X-RAY DIFFRACTION99
2.2203-2.29190.27131290.24171196X-RAY DIFFRACTION99
2.2919-2.37380.31191360.23431224X-RAY DIFFRACTION98
2.3738-2.46880.31151340.23631206X-RAY DIFFRACTION97
2.4688-2.58110.26811350.23291190X-RAY DIFFRACTION96
2.5811-2.7170.25521320.21671197X-RAY DIFFRACTION97
2.717-2.8870.28861430.23451226X-RAY DIFFRACTION98
2.887-3.10960.28141350.22241221X-RAY DIFFRACTION98
3.1096-3.4220.25421340.22671221X-RAY DIFFRACTION97
3.422-3.91580.27361300.19611233X-RAY DIFFRACTION97
3.9158-4.92830.17991380.18091207X-RAY DIFFRACTION96
4.9283-26.53810.22421410.20651226X-RAY DIFFRACTION93

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