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- PDB-3rrc: Crystal Structure of Region II from Plasmodium vivax Duffy Bindin... -

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Basic information

Entry
Database: PDB / ID: 3rrc
TitleCrystal Structure of Region II from Plasmodium vivax Duffy Binding Protein
ComponentsDuffy receptor
KeywordsCELL INVASION / Duffy Binding Like / Receptor Recognition / Duffy Antigen Receptor for Chemokines
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
PHOSPHATE ION / Duffy receptor
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsTolia, N.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Dimerization of Plasmodium vivax DBP is induced upon receptor binding and drives recognition of DARC.
Authors: Batchelor, J.D. / Zahm, J.A. / Tolia, N.H.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 27, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Duffy receptor
B: Duffy receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,34317
Polymers75,2802
Non-polymers1,06315
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-3 kcal/mol
Surface area28020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.500, 66.970, 91.830
Angle α, β, γ (deg.)90.00, 108.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Duffy receptor / Erythrocyte-binding protein


Mass: 37640.145 Da / Num. of mol.: 2 / Fragment: Region II (UNP residues 211-525)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: SaI-1 / Gene: PVDR / Production host: Escherichia coli (E. coli) / References: UniProt: P22290
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M ammonium phosphate, 23% polyethylene glycol 3350, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 22, 2008
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 50266 / Num. obs: 49943 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.05 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.703 Å / SU ML: 0.28 / σ(F): 19.05 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 2557 5.12 %RANDOM
Rwork0.195 ---
obs0.1974 49917 99.5 %-
all-50266 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.765 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7806 Å2-0 Å22.7216 Å2
2--4.4661 Å20 Å2
3----1.1396 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 64 364 5046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094771
X-RAY DIFFRACTIONf_angle_d1.0666378
X-RAY DIFFRACTIONf_dihedral_angle_d14.4681829
X-RAY DIFFRACTIONf_chiral_restr0.063665
X-RAY DIFFRACTIONf_plane_restr0.005804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98750.29831450.24592625X-RAY DIFFRACTION100
1.9875-2.0280.29251480.23782617X-RAY DIFFRACTION100
2.028-2.07210.2841240.25032590X-RAY DIFFRACTION98
2.0721-2.12020.28431410.22932607X-RAY DIFFRACTION99
2.1202-2.17320.26791300.2022624X-RAY DIFFRACTION100
2.1732-2.23180.26631320.2192656X-RAY DIFFRACTION100
2.2318-2.29740.26311550.21652592X-RAY DIFFRACTION99
2.2974-2.37150.23881320.18722605X-RAY DIFFRACTION100
2.3715-2.45610.24661350.192620X-RAY DIFFRACTION100
2.4561-2.55420.25181360.19062659X-RAY DIFFRACTION100
2.5542-2.67020.25771370.18612630X-RAY DIFFRACTION99
2.6702-2.81060.23211440.1782640X-RAY DIFFRACTION100
2.8106-2.98610.24061700.17852624X-RAY DIFFRACTION100
2.9861-3.21580.23151410.17172612X-RAY DIFFRACTION100
3.2158-3.53770.23491240.17932686X-RAY DIFFRACTION100
3.5377-4.04580.22011540.1832624X-RAY DIFFRACTION99
4.0458-5.08270.20141540.17192648X-RAY DIFFRACTION100
5.0827-19.70430.25661550.23112701X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84860.3005-0.42390.34750.11770.9240.0158-0.2630.01440.1036-0.0679-0.0071-0.01920.26410.04520.0784-0.0079-0.03710.1605-0.01250.0476-50.82399.011222.133
20.6175-0.10870.46530.2035-0.06990.91990.0090.0278-0.0373-0.0139-0.00010.0018-0.0285-0.1066-0.00950.0379-0.0246-0.02880.07950.0180.0358-44.369310.371178.1746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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