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- PDB-2xu0: Crystal structure of the NTS-DBL1(alpha-1) domain of the Plasmodi... -

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Basic information

Entry
Database: PDB / ID: 2xu0
TitleCrystal structure of the NTS-DBL1(alpha-1) domain of the Plasmodium falciparum membrane protein 1 (PfEMP1) from the varO strain.
ComponentsERYTHROCYTE MEMBRANE PROTEIN 1
KeywordsMEMBRANE PROTEIN / ADHESION / VIRULENCE / DUFFY-BINDING-LIKE-DOMAIN
Function / homology
Function and homology information


host cell surface receptor binding / membrane / metal ion binding
Similarity search - Function
Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain / PFEMP1 DBL domain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily ...Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain / PFEMP1 DBL domain / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
PROLINE / Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM PALO ALTO/UGANDA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å
AuthorsJuillerat, A. / Lewit-Bentley, A. / Guillotte, M. / Vigan-Womas, I. / Hessler, A. / Gangnard, S. / England, P. / Mercereau-Puijalon, O. / Bentley, G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of a Plasmodium Falciparum Pfemp1 Rosetting Domain Reveals a Role for the N-Terminal Segment in Heparin-Mediated Rosette Inhibition.
Authors: Juillerat, A. / Lewit-Bentley, A. / Guillotte, M. / Gangnard, S. / Hessel, A. / Baron, B. / Vigan-Womas, I. / England, P. / Mercereau-Puijalon, O. / Bentley, G.A.
History
DepositionOct 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Data collection / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERYTHROCYTE MEMBRANE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9227
Polymers56,4141
Non-polymers5086
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.248, 93.248, 126.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

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Components

#1: Protein ERYTHROCYTE MEMBRANE PROTEIN 1 / PLASMODIUM FALCIPARUM MEMBRANE PROTEIN 1


Mass: 56414.016 Da / Num. of mol.: 1 / Fragment: NTS-DBL1 DOMAIN, RESIDUES 2-487 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM PALO ALTO/UGANDA (eukaryote)
Variant: VARO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI / References: UniProt: B7T1P0
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 125 TO ALA ENGINEERED RESIDUE IN CHAIN A, THR 128 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 125 TO ALA ENGINEERED RESIDUE IN CHAIN A, THR 128 TO ALA ENGINEERED RESIDUE IN CHAIN A, THR 154 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 186 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 360 TO ALA
Sequence detailsRESIDUES 66-68 (IEG) CORRESPOND TO FACTOR X CLEAVAGE SITE. SEVEN POTENTIAL GLYCOSYLATION SITES HAVE ...RESIDUES 66-68 (IEG) CORRESPOND TO FACTOR X CLEAVAGE SITE. SEVEN POTENTIAL GLYCOSYLATION SITES HAVE BEEN MUTATED (EITHER S OR T TO A)

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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: 2.47 Å3/Da / Density % sol: 49.8 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: VAPOUR DIFFUSION WITH 10 MG/ML PROTEIN AND 0.2M NACL, WITH 1.2 MOLAR EXCESS HEPARIN 5KD, AGAINST 10% PEG3350, 0.2M L-PRO, 0.1M HEPES, PH 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11801
21801
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSOLEIL PROXIMA 110.992
SYNCHROTRONESRF ID23-120.9792
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDApr 19, 2009KB-MIRRORS
ADSC CCD2CCDKB-MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CHANNEL-CUT SI (111) CRYSTALSINGLE WAVELENGTHMx-ray1
2CHANNEL-CUT SI (111) CRYSTALSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9921
20.97921
ReflectionResolution: 2.06→34.58 Å / Num. obs: 35051 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.7
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.06→28.72 Å / Cor.coef. Fo:Fc: 0.9553 / Cor.coef. Fo:Fc free: 0.9401 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1757 5.02 %RANDOM
Rwork0.1818 ---
obs0.1835 35007 99.19 %-
Displacement parametersBiso mean: 49.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.0897 Å20 Å20 Å2
2--0.0897 Å20 Å2
3----0.1794 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: LAST / Resolution: 2.06→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 33 267 3950
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013809HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065117HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1387SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes529HARMONIC5
X-RAY DIFFRACTIONt_it3809HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion19.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion466SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4639SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.12 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2532 137 4.89 %
Rwork0.2307 2666 -
all0.2317 2803 -
obs--99.19 %

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