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- PDB-4leb: Structure of the Als3 adhesin from Candida albicans, residues 1-2... -

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Basic information

Entry
Database: PDB / ID: 4leb
TitleStructure of the Als3 adhesin from Candida albicans, residues 1-299 (mature sequence) in complex with hepta-threonine
Components
  • Agglutinin-like protein 3
  • hepta-threonine
KeywordsCELL ADHESION / adhesin / peptide binding protein / biofilm formation / cellular adhesion / peptides / cell surface
Function / homology
Function and homology information


high molecular weight kininogen binding / reductive iron assimilation / cell adhesion involved in multi-species biofilm formation / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / cell adhesion involved in biofilm formation / yeast-form cell wall / single-species biofilm formation on inanimate substrate / hyphal cell wall / adhesion of symbiont to host ...high molecular weight kininogen binding / reductive iron assimilation / cell adhesion involved in multi-species biofilm formation / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / cell adhesion involved in biofilm formation / yeast-form cell wall / single-species biofilm formation on inanimate substrate / hyphal cell wall / adhesion of symbiont to host / fungal-type cell wall / symbiont entry into host / cell adhesion involved in single-species biofilm formation / intracellular copper ion homeostasis / side of membrane / cell adhesion molecule binding / cell-cell adhesion / endocytosis / extracellular vesicle / cell adhesion / cell surface / extracellular region / plasma membrane
Similarity search - Function
Agglutinin-like protein, N-terminal domain, N2 subdomain / Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Agglutinin-like protein, N-terminal domain / Cell-wall agglutinin N-terminal ligand-sugar binding / Agglutinin-like protein / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 ...Agglutinin-like protein, N-terminal domain, N2 subdomain / Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Agglutinin-like protein, N-terminal domain / Cell-wall agglutinin N-terminal ligand-sugar binding / Agglutinin-like protein / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Agglutinin-like protein 3 / Agglutinin-like protein 3
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLin, J. / Garnett, J.A. / Cota, E.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Peptide-binding Cavity Is Essential for Als3-mediated Adhesion of Candida albicans to Human Cells.
Authors: Lin, J. / Oh, S.H. / Jones, R. / Garnett, J.A. / Salgado, P.S. / Rusnakova, S. / Matthews, S.J. / Hoyer, L.L. / Cota, E.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agglutinin-like protein 3
B: hepta-threonine


Theoretical massNumber of molelcules
Total (without water)33,1222
Polymers33,1222
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.360, 58.180, 57.180
Angle α, β, γ (deg.)90.00, 114.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Agglutinin-like protein 3 / als3 / 3D9 antigen / Adhesin 3


Mass: 32395.850 Da / Num. of mol.: 1
Fragment: sNT-Als3 (truncated N-terminal domain, UNP residues 18-316)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: ALD8, ALS3 / Plasmid: PET32 XA/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 SHuffle / References: UniProt: O74623, UniProt: Q59L12*PLUS
#2: Protein/peptide hepta-threonine


Mass: 725.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Candida albicans (yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5.6
Details: 20% v/v PEG400, 30% w/v PEG4000, 100 mM sodium citrate, 50 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 3, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.4→52.036 Å / Num. obs: 53890 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 12.095 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 6.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.7 / Num. unique all: 7562 / % possible all: 89.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LE8

4le8


Resolution: 1.4→29.09 Å / Cor.coef. Fo:Fc: 0.9724 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.986 / SU ML: 0.036 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.069 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 5405 10 %RANDOM
Rwork0.1401 ---
obs0.14046 48467 92.7676 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å21.35 Å2
2--0.74 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 0 299 2604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222525
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9293508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49624.851101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74615370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.388155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9951.51606
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0722649
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1063919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6384.5830
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.96232525
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 380 -
Rwork0.141 3384 -
obs--87.88 %

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