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

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Basic information

Entry
Database: PDB / ID: 3bqi
TitleStructure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein
ComponentsErythrocyte membrane protein 1Red blood cell
KeywordsCELL ADHESION / malaria / pregnancy / PfEMP1 / var2csa / DBL3X / chondroitin sulphate
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 / SAD / Resolution: 2.2 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)41,2552
Polymers41,1631
Non-polymers921
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.482, 86.889, 92.898
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.03 Å3/Da / Density % sol: 39.51 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→31.73 Å / Num. obs: 17198 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1997 / Rsym value: 0.448 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→31.73 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.321 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.412 / ESU R Free: 0.28
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29112 869 5.1 %RANDOM
Rwork0.22596 ---
all0.2389 16289 --
obs0.22937 16289 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 6 281 2946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9463648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.455322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3625.662136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63715512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1431510
X-RAY DIFFRACTIONr_chiral_restr0.070.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022037
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.21261
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21842
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.581.51689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02722613
X-RAY DIFFRACTIONr_scbond_it1.03231207
X-RAY DIFFRACTIONr_scangle_it1.7074.51035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 70 -
Rwork0.227 1097 -
obs--91.89 %

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