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- PDB-4gf2: Crystal structure of Plasmodium falciparum Erythrocyte Binding An... -

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Basic information

Entry
Database: PDB / ID: 4gf2
TitleCrystal structure of Plasmodium falciparum Erythrocyte Binding Antigen 140 (PfEBA-140/BAEBL)
ComponentsErythrocyte binding antigen 140
KeywordsCELL ADHESION / CELL INVASION / PfEBA-140 / BAEBL / DBL / EBL / Adhesin / Ligand / Receptor / sialic acid binding / glycophorin C
Function / homology
Function and homology information


host cell surface receptor binding / membrane
Similarity search - Function
Helix Hairpins - #1660 / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythrocyte binding antigen 140
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLin, D.H. / Malpede, B.M. / Batchelor, J.D. / Tolia, N.H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal and Solution Structures of Plasmodium falciparum Erythrocyte-binding Antigen 140 Reveal Determinants of Receptor Specificity during Erythrocyte Invasion.
Authors: Lin, D.H. / Malpede, B.M. / Batchelor, J.D. / Tolia, N.H.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Erythrocyte binding antigen 140
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,83316
Polymers73,4521
Non-polymers1,38115
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.420, 76.480, 82.340
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Erythrocyte binding antigen 140


Mass: 73451.867 Da / Num. of mol.: 1 / Fragment: UNP residues 141-755 / Mutation: S303A, T469A, S727A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8WS31
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 7, 2010
RadiationMonochromator: Unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 31532 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98

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Processing

Software
NameVersionClassification
Blu-Icedata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZRO

1zro


Resolution: 2.4→19.747 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1591 5.05 %5% of data
Rwork0.2003 ---
all0.2022 33098 --
obs0.2022 31507 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 90 143 5203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035166
X-RAY DIFFRACTIONf_angle_d0.6076867
X-RAY DIFFRACTIONf_dihedral_angle_d12.5642010
X-RAY DIFFRACTIONf_chiral_restr0.038690
X-RAY DIFFRACTIONf_plane_restr0.002871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.47750.2951320.26492675X-RAY DIFFRACTION99
2.4775-2.56590.32491460.26182713X-RAY DIFFRACTION99
2.5659-2.66840.3071450.24762707X-RAY DIFFRACTION100
2.6684-2.78950.25751460.23172692X-RAY DIFFRACTION99
2.7895-2.93620.2531470.22142722X-RAY DIFFRACTION100
2.9362-3.11950.25841310.21632714X-RAY DIFFRACTION100
3.1195-3.35920.27541400.20942737X-RAY DIFFRACTION100
3.3592-3.69530.2351600.18912707X-RAY DIFFRACTION100
3.6953-4.22540.21941340.17382738X-RAY DIFFRACTION100
4.2254-5.30640.20661470.1812740X-RAY DIFFRACTION99
5.3064-19.74780.21531630.19682771X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.59970.0364-0.06484.8987-0.21845.0219-0.2460.15751.11380.17810.1062-0.5281-0.62360.0276-0.04410.41630.05320.02110.27280.13710.7081-2.96928.732410.5186
25.3504-0.40530.18934.3941-0.21112.9272-0.01250.17390.41220.0036-0.1391-0.8891-0.02680.32410.09430.28160.05460.01510.28490.09230.51522.9757-1.208613.4982
37.3527-1.54334.23511.2414-1.2771.75810.34990.5152-0.3039-0.5652-0.18790.09490.45590.1907-0.21570.59560.01420.03530.51870.0970.3268-19.3029-2.783-8.2698
42.9647-1.56151.05447.3498-2.31023.21820.196-0.1667-0.386-0.38420.01890.63560.2470.0032-0.22350.3162-0.0248-0.03170.3481-0.04010.2989-45.527215.7215-27.7829
54.82730.59861.71715.5024-0.15933.62830.26650.462-0.0583-0.8239-0.0765-0.3320.24440.5551-0.18480.38870.06840.08540.4169-0.01960.2704-37.152119.4006-29.936
66.4458-0.92922.15263.12590.70123.6038-0.02041.1151-0.1596-1.1629-0.13850.7509-0.270.15510.13791.00170.0936-0.18770.60210.03230.6186-55.761127.9103-49.435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 143:193
2X-RAY DIFFRACTION2chain A and resseq 194:312
3X-RAY DIFFRACTION3chain A and resseq 313:422
4X-RAY DIFFRACTION4chain A and resseq 423:500
5X-RAY DIFFRACTION5chain A and resseq 501:606
6X-RAY DIFFRACTION6chain A and resseq 607:740

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