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- PDB-2rji: Malarial EBA-175 region VI crystallographic structure reveals a K... -

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Basic information

Entry
Database: PDB / ID: 2rji
TitleMalarial EBA-175 region VI crystallographic structure reveals a KIX-like binding interface
ComponentsErythrocyte binding antigen 175
KeywordsPROTEIN TRANSPORT / CELL INVASION / CBP KIX / EBA-175 / Plasmodium falciparum / region VI
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
Erythrocyte binding antigen 175 region VI / Erythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Rna Polymerase Sigma Factor; Chain: A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythrocyte binding protein / Erythrocyte binding antigen 175
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWithers-Martinez, C. / Blackman, M.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Malarial EBA-175 Region VI Crystallographic Structure Reveals a KIX-Like Binding Interface
Authors: Withers-Martinez, C. / Haire, L.F. / Hackett, F. / Walker, P.A. / Howell, S.A. / Smerdon, S.J. / Dodson, G.G. / Blackman, M.J.
History
DepositionOct 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythrocyte binding antigen 175
B: Erythrocyte binding antigen 175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0613
Polymers20,0202
Non-polymers401
Water1,35175
1
A: Erythrocyte binding antigen 175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0502
Polymers10,0101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Erythrocyte binding antigen 175


Theoretical massNumber of molelcules
Total (without water)10,0101
Polymers10,0101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.237, 65.591, 105.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-112-

HOH

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Components

#1: Protein Erythrocyte binding antigen 175


Mass: 10010.240 Da / Num. of mol.: 2 / Fragment: UNP residues 1307-1389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: eba175reVIsynth / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q9NG63, UniProt: Q25842*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M citric acid, 1M LiCl, 25-30% PEG 6K, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSRS PX10.110.977
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDMay 23, 2007mirrors
RIGAKU RAXIS IV++2IMAGE PLATEMay 23, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1a double crystal Si(III) monochromator with horizontal saggital focusing systemSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
21.541
ReflectionResolution: 1.8→30 Å / Num. obs: 16406 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.3
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2030 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.549 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24114 834 5.1 %RANDOM
Rwork0.20832 ---
obs0.21003 15553 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 1 75 1384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221341
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9531813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1585160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60524.68864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87815235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.318155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02995
X-RAY DIFFRACTIONr_nbd_refined0.20.2660
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.26
X-RAY DIFFRACTIONr_mcbond_it1.721.5839
X-RAY DIFFRACTIONr_mcangle_it2.64921321
X-RAY DIFFRACTIONr_scbond_it3.5683575
X-RAY DIFFRACTIONr_scangle_it5.154.5492
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 53 -
Rwork0.292 1119 -
obs--99.41 %

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