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- PDB-2y8d: STRUCTURE OF DBL6 EPSILON DOMAIN FROM VAR2CSA STRAIN FCR3 -

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Basic information

Entry
Database: PDB / ID: 2y8d
TitleSTRUCTURE OF DBL6 EPSILON DOMAIN FROM VAR2CSA STRAIN FCR3
ComponentsERYTHROCYTE MEMBRANE PROTEIN 1Red blood cell
KeywordsMEMBRANE PROTEIN / DBL EPSILON / PFEMP1 / MALARIA
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Duffy-antigen binding domain / 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 / 5 helical Cullin repeat like / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Duffy-antigen binding domain / 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 / 5 helical Cullin repeat like / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZAMIDINE / 2-AMINO-ETHANETHIOL / Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsGangnard, S. / Ramboarina, S. / Lewit-Bentley, A. / Bentley, G.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural and Immunological Correlations between the Variable Blocks of the Var2Csa Domain Dbl6Epsilon from Two Plasmodium Falciparum Parasite Lines.
Authors: Gangnard, S. / Badaut, C. / Ramboarina, S. / Baron, B. / Ramdani, T. / Gamain, B. / Deloron, P. / Lewit-Bentley, A. / Bentley, G.A.
History
DepositionFeb 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3May 15, 2013Group: Database references
Revision 1.4Mar 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 / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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)36,5434
Polymers36,2691
Non-polymers2743
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.859, 56.229, 75.849
Angle α, β, γ (deg.)90.00, 123.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3629-

BEN

21A-3629-

BEN

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Components

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


Mass: 36268.898 Da / Num. of mol.: 1 / Fragment: DBL6 EPSILON, RESIDUES 2326-2631
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: FCR3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SHUFFLE / References: UniProt: Q6UDW7
#2: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE / Cysteamine


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NS
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBENZAMIDINE (BDN): THE BENZAMIDINE MOIETY LIES ON A TWO-FOLD AXIS

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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: 2.22 Å3/Da / Density % sol: 44.13 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: 30% PEG 4000, 0.1M NA ACETATE, PH 4.8, 0.1M MGCL2, 2.6% BENZAMIDINE, 10MG/ML PROTEIN IN 0.02M TRIS PH 8, 0.14M NACL, 0.045M CYSTAMINE; VAPOUR DIFFUSION

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Data collection

DiffractionMean temperature: 180 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: 1.84→35.2 Å / Num. obs: 24727 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 38.74 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.6 / % possible all: 73.7

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Processing

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

2wau


Resolution: 1.84→43.92 Å / Cor.coef. Fo:Fc: 0.9527 / Cor.coef. Fo:Fc free: 0.9375 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1267 5.12 %RANDOM
Rwork0.2034 ---
obs0.2051 24727 93.55 %-
Displacement parametersBiso mean: 53.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.3029 Å20 Å2-0.2318 Å2
2--0.8351 Å20 Å2
3---1.4679 Å2
Refine analyzeLuzzati coordinate error obs: 0.271 Å
Refinement stepCycle: LAST / Resolution: 1.84→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 17 112 2446
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112413HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053236HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d884SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes331HARMONIC5
X-RAY DIFFRACTIONt_it2413HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion21.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion299SEMIHARMONIC5
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_contact2917SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.92 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2266 105 5.38 %
Rwork0.2358 1848 -
all0.2353 1953 -
obs--93.55 %

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