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- PDB-2wau: Structure of DBL6 epsilon domain from VAR2CSA -

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Basic information

Entry
Database: PDB / ID: 2wau
TitleStructure of DBL6 epsilon domain from VAR2CSA
ComponentsERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1)Red blood cell
KeywordsMEMBRANE PROTEIN / CHONDROITIN SULPHATE A / MEMBRANE PROTEIN DBL / PFEMP1 / MALARIA / VAR2CSA
Function / homology
Function and homology information


modulation by symbiont of host erythrocyte aggregation / infected host cell surface knob / antigenic variation / adhesion of symbiont to microvasculature / cell adhesion molecule binding / cell-cell adhesion / host cell surface receptor binding / host cell plasma membrane / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Duffy-antigen binding domain / Duffy-binding-like domain / PFEMP1 DBL 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Duffy-antigen binding domain / Duffy-binding-like domain / PFEMP1 DBL 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
Erythrocyte membrane protein 1, PfEMP1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsKhunrae, P. / Higgins, M.K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural Comparison of Two Cspg-Binding Dbl Domains from the Var2Csa Protein Important in Malaria During Pregnancy.
Authors: Khunrae, P. / Philip, J.M.D. / Bull, D.R. / Higgins, M.K.
History
DepositionFeb 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 3, 2014Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1)
B: ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1)


Theoretical massNumber of molelcules
Total (without water)71,2672
Polymers71,2672
Non-polymers00
Water0
1
A: ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1)


Theoretical massNumber of molelcules
Total (without water)35,6331
Polymers35,6331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1)


Theoretical massNumber of molelcules
Total (without water)35,6331
Polymers35,6331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.943, 62.943, 334.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1) / Red blood cell / VAR2CSA


Mass: 35633.297 Da / Num. of mol.: 2 / Fragment: DBL6 EPSILON, RESIDUES 2333-2634 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Description: GENOMIC DNA FROM MR4 / Cell: ERYTHROCYTE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8I639
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 2480 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 2480 TO SER
Sequence detailsTHE STRUCTURE IS OF THE C2480S MUTANT.

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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: 2.33 Å3/Da / Density % sol: 46.8 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONDiamond I0210.92
SYNCHROTRONESRF BM1420.97855, 0.97871, 0.91999
Detector
TypeIDDetectorDate
ADSC CCD1CCDAug 8, 2008
MARRESEARCH2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.978551
30.978711
40.919991
ReflectionResolution: 3→111.1 Å / Num. obs: 14481 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3→83.62 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.855 / SU B: 60.736 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.572
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.325 723 5 %RANDOM
Rwork0.289 ---
obs0.29 13680 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 3→83.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 0 0 4541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224644
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8931.9486232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7035544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93125.519241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22815915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0011518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023494
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.22060
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23191
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2871.52825
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23524398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.78132133
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9544.51834
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 54
Rwork0.37 952

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