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- PDB-1zrl: Crystal structure of EBA-175 Region II (RII) -

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Basic information

Entry
Database: PDB / ID: 1zrl
TitleCrystal structure of EBA-175 Region II (RII)
Componentserythrocyte binding antigen region II
KeywordsCELL INVASION / EBA-175 / RII / DBL / erythrocyte / invasion / host / malaria / disease / glycophorin / glycan / sialic acid
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
Helix Hairpins - #1660 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythrocyte binding antigen region II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, CROSS CRYSTAL AVERAGING / Resolution: 2.3 Å
AuthorsTolia, N.H. / Enemark, E.J. / Sim, B.K. / Joshua-Tor, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structural Basis for the EBA-175 Erythrocyte Invasion Pathway of the Malaria Parasite Plasmodium falciparum.
Authors: Tolia, N.H. / Enemark, E.J. / Sim, B.K. / Joshua-Tor, L.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: erythrocyte binding antigen region II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,08411
Polymers72,1841
Non-polymers90010
Water5,873326
1
A: erythrocyte binding antigen region II
hetero molecules

A: erythrocyte binding antigen region II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,16922
Polymers144,3692
Non-polymers1,80020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area6720 Å2
ΔGint-261 kcal/mol
Surface area60750 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.645, 103.645, 212.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsBiological assembly is a dimer generated by the crystallographic two fold axis: -x, y, -z.

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Components

#1: Protein erythrocyte binding antigen region II / EBA-175 Region II (RII)


Mass: 72184.391 Da / Num. of mol.: 1 / Mutation: N3Q, S50A, S195A, T206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Pichia pastoris (fungus) / References: UniProt: Q25735
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.881 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: high salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
2,11
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X26C21.0393, 1.0397
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2MADMx-ray1
1Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.03931
31.03971
ReflectionResolution: 2.3→36.65 Å / Num. obs: 53219 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.6 / % possible all: 92.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD, CROSS CRYSTAL AVERAGING / Resolution: 2.3→36.65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 582146.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2295 5 %RANDOM
Rwork0.232 ---
obs0.232 46272 88.3 %-
all-53219 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.3171 Å2 / ksol: 0.340333 e/Å3
Displacement parametersBiso mean: 50.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--1.92 Å20 Å2
3----3.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 46 326 5280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 329 5.1 %
Rwork0.303 6166 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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