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- PDB-2ylh: Structure of N-terminal domain of Candida albicans Als9-2 G299W mutant -

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Basic information

Entry
Database: PDB / ID: 2ylh
TitleStructure of N-terminal domain of Candida albicans Als9-2 G299W mutant
ComponentsAGGLUTININ-LIKE PROTEIN
KeywordsCELL ADHESION / ADHESIN / PEPTIDE-BINDING PROTEIN
Function / homology
Function and homology information


cell adhesion involved in multi-species biofilm formation / hyphal growth / single-species biofilm formation on inanimate substrate / yeast-form cell wall / hyphal cell wall / cell adhesion involved in single-species biofilm formation / side of membrane / cell-cell adhesion / extracellular vesicle / cell adhesion ...cell adhesion involved in multi-species biofilm formation / hyphal growth / single-species biofilm formation on inanimate substrate / yeast-form cell wall / hyphal cell wall / cell adhesion involved in single-species biofilm formation / side of membrane / cell-cell adhesion / extracellular vesicle / cell adhesion / cell surface / 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 9 / Agglutinin-like protein
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSalgado, P.S. / Burchell, L. / Cota, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural Basis for the Broad Specificity to Host- Cell Ligands by the Pathogenic Fungus Candida Albicans.
Authors: Salgado, P.S. / Yan, R. / Taylor, J.D. / Burchell, L. / Jones, R. / Hoyer, L.L. / Matthews, S.J. / Simpson, P.J. / Cota, E.
History
DepositionJun 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,6751
Polymers33,6751
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.200, 68.700, 121.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGGLUTININ-LIKE PROTEIN


Mass: 33675.098 Da / Num. of mol.: 1 / Fragment: NT_ALS9-2 N-TERMINAL DOMAIN, RESIDUES 18-328 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: PET32XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ORIGAMI B / References: UniProt: Q9C471, UniProt: A0A1D8PQ86*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 313 TO TRP
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: 2.2 Å3/Da / Density % sol: 43.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.12713
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.7→33.05 Å / Num. obs: 32813 / % possible obs: 97.8 % / Observed criterion σ(I): 5.5 / Redundancy: 5.2 % / Biso Wilson estimate: 21.917 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.88 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y7N

2y7n


Resolution: 1.7→33.05 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.921 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23664 1639 5 %RANDOM
Rwork0.20617 ---
obs0.20772 31127 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 0 380 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222422
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9313322
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07525.15597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39815350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.458154
X-RAY DIFFRACTIONr_chiral_restr0.1250.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211839
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 116 -
Rwork0.265 2209 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -4.257 Å / Origin y: 11.618 Å / Origin z: -16.694 Å
111213212223313233
T0.0168 Å20.0024 Å2-0.0054 Å2-0.0214 Å20.0106 Å2--0.0081 Å2
L0.0513 °2-0.0457 °2-0.0012 °2-0.6623 °2-0.3204 °2--0.1705 °2
S-0.005 Å °-0.0187 Å °-0.0058 Å °0.0109 Å °-0.0008 Å °-0.0034 Å °-0.0111 Å °0.0067 Å °0.0058 Å °

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