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- PDB-3cpz: Crystal structure of VAR2CSA DBL3x domain in the presence of dode... -

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Basic information

Entry
Database: PDB / ID: 3cpz
TitleCrystal structure of VAR2CSA DBL3x domain in the presence of dodecasaccharide of CSA
ComponentsErythrocyte membrane protein 1Red blood cell
KeywordsMEMBRANE PROTEIN / DBL3x / VAR2CSA / Chondroitin sulphate A (CSA) / pregnancy-associated malaria
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: 2.8 Å
AuthorsSingh, K. / Gittis, A.G. / Nguyen, P. / Gowda, D.C. / Miller, L.H. / Garboczi, D.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A.
Authors: Singh, K. / Gittis, A.G. / Nguyen, P. / Gowda, D.C. / Miller, L.H. / Garboczi, D.N.
History
DepositionApr 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)41,5572
Polymers41,4611
Non-polymers961
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.520, 86.760, 101.570
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


Mass: 41460.730 Da / Num. of mol.: 1 / Fragment: DBL3x domain (UNP residues 1220-1580)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: A4 / Gene: var / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q6UDW7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Nonpolymer detailsLIGAND USED IN THE CRYSTALLIZATION WAS A DODECASSACHARIDE OF CHONDROITIN SULFATE A WHICH IS A ...LIGAND USED IN THE CRYSTALLIZATION WAS A DODECASSACHARIDE OF CHONDROITIN SULFATE A WHICH IS A SULFATED GLYCOSAMINOGLYCAN (GAG) COMPOSED OF A CHAIN OF ALTERNATING SUGARS D-GLUCURONIC ACID BETA (1-3 LINKAGE) AND D-N-ACETYL GALACTOSAMINE BETA (1-4 LINKAGE). THEY ARE SULFATED AT POSITIONS 4 OF N-ACETYL GALACTOSAMINE. ONLY SULFATE WAS MODELED DUE TO LACK OF GOOD ELECTRON DENSITY FOR THE REST OF THE LIGAND.

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.1M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 20, 2007
Details: two Double-crystal monochromators Si-111 and Si-220
RadiationMonochromator: Two double-crystal monochromators Si-111 and Si-220
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 9717 / Num. obs: 9572 / % possible obs: 98.5 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 12.5
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.85 / Num. unique all: 1427 / Rsym value: 0.435 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CML

3cml


Resolution: 2.8→19.61 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1592007.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.353 772 8.1 %RANDOM
Rwork0.299 ---
obs0.299 9572 98.4 %-
all-9717 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.3502 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 72.8 Å2
Baniso -1Baniso -2Baniso -3
1-29.93 Å20 Å20 Å2
2---26.89 Å20 Å2
3----3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 5 0 2247
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.517 123 7.9 %
Rwork0.407 1427 -
obs-1427 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3so4.paramso4.top

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