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- PDB-4p1t: Crystal structure of the DBL3X-DBL4epsilon double domain from the... -

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Basic information

Entry
Database: PDB / ID: 4p1t
TitleCrystal structure of the DBL3X-DBL4epsilon double domain from the extracellular part of VAR2CSA PfEMP1 from Plasmodium falciparum
ComponentsErythrocyte membrane protein 1
KeywordsMEMBRANE PROTEIN / PfEMP1 / CSA / DBL fold
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
Plasmodium falciparum erythrocyte membrane protein 1, N-terminal / N-terminal segments of P. falciparum erythrocyte membrane protein / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsGangnard, S. / Dechavanne, S. / Srivastava, A. / Amirat, F. / Gamain, B. / Lewit-Bentley, A. / Bentley, G.A.
CitationJournal: Sci Rep / Year: 2015
Title: Structure of the DBL3X-DBL4 epsilon region of the VAR2CSA placental malaria vaccine candidate: insight into DBL domain interactions.
Authors: Gangnard, S. / Lewit-Bentley, A. / Dechavanne, S. / Srivastava, A. / Amirat, F. / Bentley, G.A. / Gamain, B.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythrocyte membrane protein 1


Theoretical massNumber of molelcules
Total (without water)86,4401
Polymers86,4401
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.794, 129.336, 64.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Erythrocyte membrane protein 1


Mass: 86439.617 Da / Num. of mol.: 1
Fragment: DBL3X-DBL4epsilon double domain (UNP residues 1215-1950)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: FCR-3 / Gene: var2csa / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: Q6UDW7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.294 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 3000, 100 mM Bis-Tris buffer, 300 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 27, 2011 / Details: KB-MIRRORS
RadiationMonochromator: CHANNEL-CUT SI (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.9→28.16 Å / Num. obs: 17568 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 56.41 Å2 / Rmerge(I) obs: 0.263 / Rsym value: 0.243 / Net I/av σ(I): 3.1 / Net I/σ(I): 6.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 0.8 / % possible all: 92.1

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Processing

SoftwareName: BUSTER / Version: 2.11.4 / Classification: refinement
RefinementResolution: 2.9→28.16 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.821 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.436
RfactorNum. reflection% reflectionSelection details
Rfree0.276 903 5.16 %RANDOM
Rwork0.203 ---
obs0.207 17510 92.21 %-
Displacement parametersBiso mean: 60.75 Å2
Baniso -1Baniso -2Baniso -3
1-15.8807 Å20 Å20 Å2
2--12.2196 Å20 Å2
3----28.1003 Å2
Refine analyzeLuzzati coordinate error obs: 0.361 Å
Refinement stepCycle: final / Resolution: 2.9→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 0 14 5090
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015200HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.247037HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1777SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes739HARMONIC5
X-RAY DIFFRACTIONt_it5200HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion24.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion685SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6146SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2607 102 5.67 %
Rwork0.2265 1697 -
all0.2285 1799 -
obs--92.21 %

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