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

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Basic information

Entry
Database: PDB / ID: 4jno
TitleCrystal structure of Plasmodium falciparum Erythrocyte Binding Antigen 140 (PfEBA-140/BAEBL) Region II in complex with sialyllactose
ComponentsBAEBL protein
KeywordsCELL ADHESION / DBL domain / Glycophorin C / Extracellular / sialic acid binding
Function / homology
Function and homology information


: / membrane => GO:0016020 / 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
N-acetyl-alpha-neuraminic acid / BAEBL protein / Erythrocyte binding antigen 140
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTolia, N.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular Basis for Sialic Acid-dependent Receptor Recognition by the Plasmodium falciparum Invasion Protein Erythrocyte-binding Antigen-140/BAEBL.
Authors: Malpede, B.M. / Lin, D.H. / Tolia, N.H.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAEBL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0703
Polymers73,4521
Non-polymers6192
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.950, 76.030, 81.430
Angle α, β, γ (deg.)90.00, 96.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BAEBL protein / Erythrocyte binding antigen region II / Erythrocyte binding protein-2


Mass: 73451.867 Da / Num. of mol.: 1 / Mutation: S303A, T469A, S727A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: EBP2, eba-140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T9N3, UniProt: Q8WS31*PLUS
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
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: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→29.724 Å / Num. obs: 15336 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.09 Å / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 769 5.01 %RANDOM
Rwork0.2182 ---
obs0.2201 15336 96.27 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 0 42 22 4959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0015046
X-RAY DIFFRACTIONf_angle_d0.4376736
X-RAY DIFFRACTIONf_dihedral_angle_d10.2841967
X-RAY DIFFRACTIONf_chiral_restr0.03690
X-RAY DIFFRACTIONf_plane_restr0.001859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23140.37021410.31242952X-RAY DIFFRACTION98
3.2314-3.55610.29791690.26722901X-RAY DIFFRACTION97
3.5561-4.06960.25611450.21192916X-RAY DIFFRACTION97
4.0696-5.1230.23421510.19192911X-RAY DIFFRACTION96
5.123-29.72550.22141630.19622887X-RAY DIFFRACTION94
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)
18.4144-0.00781.6835.9080.62847.0396-0.37190.15640.9553-0.41450.0232-0.0849-1.0327-0.15740.24510.43880.00070.00780.2620.17910.865-2.81978.83257.9308
25.7180.9729-0.68765.0425-1.063.33880.0169-0.07990.3922-0.0037-0.0239-0.74580.03330.38280.00030.3760.04760.01220.32180.07770.68093.1136-1.117913.3323
36.0207-2.97542.53874.0197-0.9121.68250.22420.4101-0.1125-0.5189-0.14110.30640.5858-0.0257-0.07320.5349-0.01770.01070.42360.06260.4691-19.2864-2.7519-8.2873
45.469-1.23350.97637.2747-3.50554.74090.2358-0.3035-0.5508-0.31070.17090.56480.2765-0.1904-0.28350.3465-0.0219-0.09930.4348-0.12990.6277-45.353515.4841-27.8231
55.08650.12590.62776.37521.62325.97970.28910.1997-0.0576-0.6726-0.1156-0.54680.08920.4953-0.17520.3260.08440.10410.4215-0.01890.5261-37.023319.3723-29.8217
68.34690.3613.37771.1285-0.36894.0633-0.08750.8986-0.1127-0.90440.00850.5505-0.20510.15270.15510.88980.1238-0.10620.6134-0.02150.7862-55.413527.9474-49.1395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 148:193
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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