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- PDB-3c64: The MC179 portion of the Cysteine-rich Interdomain Region (CIDR) ... -

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Basic information

Entry
Database: PDB / ID: 3c64
TitleThe MC179 portion of the Cysteine-rich Interdomain Region (CIDR) of a Plasmodium falciparum Erythrocyte Membrane Protein-1 (PfEMP1)
ComponentsPfEMP1 variant 2 of strain MC
KeywordsCD36-BINDING PROTEIN / CELL ADHESION / ALPHA-HELICAL / THREE-Helix Bundle
Function / homology
Function and homology information


host cell surface / host cell surface receptor binding / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / 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
PfEMP1 variant 1 of strain MC / PfEMP1 variant 2 of strain MC
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å
AuthorsKlein, M.M. / Gittis, A.G. / Su, H.P. / Makobongo, M.O. / Moore, J.M. / Singh, S. / Miller, L.H. / Garboczi, D.N.
CitationJournal: Plos Pathog. / Year: 2008
Title: The Cysteine-Rich Interdomain Region from the Highly Variable Plasmodium falciparum Erythrocyte Membrane Protein-1 Exhibits a Conserved Structure.
Authors: Klein, M.M. / Gittis, A.G. / Su, H.P. / Makobongo, M.O. / Moore, J.M. / Singh, S. / Miller, L.H. / Garboczi, D.N.
History
DepositionFeb 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PfEMP1 variant 2 of strain MC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1623
Polymers20,9321
Non-polymers2302
Water41423
1
A: PfEMP1 variant 2 of strain MC
hetero molecules

A: PfEMP1 variant 2 of strain MC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3236
Polymers41,8642
Non-polymers4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area5110 Å2
ΔGint-63.3 kcal/mol
Surface area18620 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.31, 93.31, 85.71
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PfEMP1 variant 2 of strain MC


Mass: 20932.031 Da / Num. of mol.: 1 / Fragment: UNP residues 576-754
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: Malayan Camp / Gene: MCvar-2 PfEMP1 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-(RIL) / References: UniProt: Q25734, UniProt: Q25733*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 27% PEG 400, 100MM NACL, 50MM SODIUM CITRATE, pH 4.20, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 23, 2003 / Details: Osmic Blue multilayer optic
RadiationMonochromator: blue osmic multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 9053 / Num. obs: 9044 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 18.2 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 18.8
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 748 -RANDOM
Rwork0.246 ---
obs0.246 9044 99.9 %-
all-9053 --
Displacement parametersBiso mean: 42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati sigma a0.43 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 14 23 1295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d1.59

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