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- PDB-3cml: Crystal Structure of the DBL3x domain of the Plasmodium falcipuru... -

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Basic information

Entry
Database: PDB / ID: 3cml
TitleCrystal Structure of the DBL3x domain of the Plasmodium falcipurum VAR2CSA protein
ComponentsErythrocyte membrane protein 1Red blood cell
KeywordsMEMBRANE PROTEIN / DBL3x / VAR2CSA / chondroitin-sulfate binding domain
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: 1.9 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
DepositionMar 23, 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


Theoretical massNumber of molelcules
Total (without water)41,4611
Polymers41,4611
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.670, 84.200, 86.490
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: IT4 / Gene: var / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q6UDW7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.785878 Å3/Da / Density % sol: 31.126314 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-25% PEG 3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2007
RadiationMonochromator: double crystal Si (220) cryogenically cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 24118 / Num. obs: 23884 / % possible obs: 98.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.627 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C6J

2c6j
PDB Unreleased entry


Resolution: 1.9→19.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1401715.44 / 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
Rfree0.253 1880 7.9 %RANDOM
Rwork0.223 ---
obs0.223 23884 98.9 %-
all-24118 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6626 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å20 Å20 Å2
2---1.78 Å20 Å2
3----2.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 98 2465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 293 7.8 %
Rwork0.327 3458 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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