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- PDB-2yk0: Structure of the N-terminal NTS-DBL1-alpha and CIDR-gamma double ... -

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Basic information

Entry
Database: PDB / ID: 2yk0
TitleStructure of the N-terminal NTS-DBL1-alpha and CIDR-gamma double domain of the PfEMP1 protein from Plasmodium falciparum varO strain.
ComponentsERYTHROCYTE MEMBRANE PROTEIN 1Red blood cell
KeywordsMEMBRANE PROTEIN / ADHESIN / PFEMP1
Function / homology
Function and homology information


host cell surface receptor binding / membrane / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1930 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1930 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLewit-Bentley, A. / Juillerat, A. / Vigan-Womas, I. / Guillotte, M. / Hessel, A. / Raynal, B. / Mercereau-Puijalon, O. / Bentley, G.A.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Basis for the Abo Blood-Group Dependence of Plasmodium Falciparum Rosetting.
Authors: Vigan-Womas, I. / Guillotte, M. / Juillerat, A. / Hessel, A. / Raynal, B. / England, P. / Cohen, J.H. / Bertrand, O. / Peyrard, T. / Bentley, G.A. / Lewit-Bentley, A. / Mercereau-Puijalon, O.
History
DepositionMay 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: ERYTHROCYTE MEMBRANE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1065
Polymers91,8661
Non-polymers2414
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.907, 144.362, 75.836
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ERYTHROCYTE MEMBRANE PROTEIN 1 / Red blood cell


Mass: 91865.680 Da / Num. of mol.: 1 / Fragment: DBL1-CIDR, RESIDUES 2-787 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: PALO ALTO / Variant: VARO / Plasmid: PMAL-C2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA GAMI / References: UniProt: B7T1P0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 10 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 125 TO SER ...ENGINEERED RESIDUE IN CHAIN A, THR 10 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 125 TO SER 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 ENGINEERED RESIDUE IN CHAIN A, SER 657 TO ALA
Sequence detailsRESIDUES 66-68 (IEG) CORRESPOND TO FACTOR X CLEAVAGE SITE AND EIGHT POTENTIAL GLYCOSYLATION SITES ...RESIDUES 66-68 (IEG) CORRESPOND TO FACTOR X CLEAVAGE SITE AND EIGHT POTENTIAL GLYCOSYLATION SITES HAVE BEEN MUTATED (EITHER SER OR THR TO ALA).

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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: 5.25 Å3/Da / Density % sol: 76.4 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: VAPOUR DIFFUSION, 10 MG/ML PROTEIN AGAINST 10% PEG 3350, 200 MM NACL, 100 MM SODIUM CITRATE PH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2010 / Details: KB-MIRRORS
RadiationMonochromator: CHANNEL-CUT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 39458 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 67.08 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.8 / % possible all: 84.7

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XU0

2xu0


Resolution: 2.8→40.23 Å / Cor.coef. Fo:Fc: 0.8467 / Cor.coef. Fo:Fc free: 0.816 / SU R Cruickshank DPI: 0.353 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.329 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 2007 5.09 %RANDOM
Rwork0.2127 ---
obs0.2148 39458 96.82 %-
Displacement parametersBiso mean: 76.52 Å2
Baniso -1Baniso -2Baniso -3
1--38.5522 Å20 Å2-18.0451 Å2
2--11.6573 Å20 Å2
3---26.8948 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 12 32 5710
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.247847HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2117SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes181HARMONIC2
X-RAY DIFFRACTIONt_gen_planes821HARMONIC5
X-RAY DIFFRACTIONt_it5827HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion25.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion735SEMIHARMONIC5
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_contact6849SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3181 101 4.08 %
Rwork0.2621 2372 -
all0.2645 2473 -
obs--96.82 %

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