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- PDB-3bqk: Structure of a chondroitin sulphate binding DBL3X from a var2csa ... -

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Basic information

Entry
Database: PDB / ID: 3bqk
TitleStructure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein in complex with sulphate
ComponentsErythrocyte membrane protein 1Red blood cell
KeywordsCELL ADHESION / malaria / pregnancy / var2csa encoded PfEMP1 protein / DBL3X domain / chondroitin sulphate A
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
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 ...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 / 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: 1.8 Å
AuthorsHiggins, M.K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The structure of a chondroitin sulfate-binding domain important in placental malaria.
Authors: Higgins, M.K.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 19, 2014Group: Database references

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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)41,3513
Polymers41,1631
Non-polymers1882
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.258, 86.555, 92.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Erythrocyte membrane protein 1 / Red blood cell / PfEMP1 protein


Mass: 41163.320 Da / Num. of mol.: 1 / Fragment: DBL3X domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: A4 / Gene: var / Plasmid: pEt15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: Q6UDW7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4K, 20mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Aug 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→63 Å / Num. obs: 31419 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4507 / Rsym value: 0.791 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.18 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.054 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.166
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28647 1575 5 %RANDOM
Rwork0.23093 ---
obs0.23382 29784 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.148 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 11 232 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222793
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9493750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8115333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60925.755139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25815532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.691510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022093
X-RAY DIFFRACTIONr_nbd_refined0.20.21426
X-RAY DIFFRACTIONr_nbtor_refined0.30.21916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.221
X-RAY DIFFRACTIONr_mcbond_it0.6631.51743
X-RAY DIFFRACTIONr_mcangle_it1.05522687
X-RAY DIFFRACTIONr_scbond_it1.41931238
X-RAY DIFFRACTIONr_scangle_it2.1624.51063
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 115 -
Rwork0.3 2163 -
obs--99.91 %

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