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- PDB-6rha: Crystal structure of the amyloid-like NTVTFN segment from the Can... -

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Basic information

Entry
Database: PDB / ID: 6rha
TitleCrystal structure of the amyloid-like NTVTFN segment from the Candida albicans Agglutinin-like protein (Adhesin) 5
ComponentsAgglutinin-like protein 5
KeywordsPROTEIN FIBRIL / Bacterial steric-zipper cross-beta amyloid fibril from Candida albicans
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 surface / plasma membrane
Similarity search - Function
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 / Fibrogen-binding domain 1 / Adhesion domain superfamily
Similarity search - Domain/homology
Agglutinin-like protein 5
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
Model detailsAdhesin
AuthorsLandau, M. / Perov, S.
CitationJournal: To be published
Title: Amyloid structures from a Candida albicans adhesin Structure and conservation of amyloid spines from fungal adhesins
Authors: Perov, S. / Landau, M. / Lipke, P.N.
History
DepositionApr 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Agglutinin-like protein 5
A: Agglutinin-like protein 5


Theoretical massNumber of molelcules
Total (without water)1,3892
Polymers1,3892
Non-polymers00
Water905
1
B: Agglutinin-like protein 5
A: Agglutinin-like protein 5
x 9


Theoretical massNumber of molelcules
Total (without water)12,50518
Polymers12,50518
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_155x-4,y,z1
crystal symmetry operation1_255x-3,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_955x+4,y,z1
Unit cell
Length a, b, c (Å)4.870, 39.810, 20.260
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Agglutinin-like protein 5 / Adhesin 5


Mass: 694.733 Da / Num. of mol.: 2
Fragment: Amyloid spine segment NTVTFN from Als5 (residues 156-161) secreted by Candida albicans
Source method: obtained synthetically / Details: NTVTFN from Als5, synthesized / Source: (synth.) Candida albicans (yeast) / References: UniProt: O13368
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir contained 0.1M HEPES 7.5 pH, 0.8 M NaH2PO4, and 0.8M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.6→19.91 Å / Num. obs: 991 / % possible obs: 98.2 % / Redundancy: 14.28 % / Biso Wilson estimate: 19.469 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.27 / Rrim(I) all: 0.28 / Χ2: 0.747 / Net I/σ(I): 7.3 / Num. measured all: 14151 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.697.0871.0052.28931401260.7271.08490
1.69-1.796.840.8152.918551251250.7470.883100
1.79-1.9117.0980.8414.2620861221220.9460.869100
1.91-2.0716.6920.4557.1122201331330.9580.47100
2.07-2.2617.5280.388.3421561231230.9820.392100
2.26-2.5317.0350.2939.7619251151130.9920.30298.3
2.53-2.9218.0680.2969.42133774740.9850.305100
2.92-3.5815.2310.18512.76118878780.9950.191100
3.58-5.0615.0410.17114.02109874730.9610.17898.6
5.06-19.9116.3750.14511.9439325240.9870.15196

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation1.6 Å19.91 Å
Translation1.6 Å19.91 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.5.1phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: beta strand

Resolution: 1.6→19.91 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.893 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.121
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 99 10 %RANDOM
Rwork0.1984 ---
obs0.1998 891 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 31.18 Å2 / Biso mean: 10.562 Å2 / Biso min: 6.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20.05 Å2
2--0.21 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.6→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms98 0 0 5 103
Biso mean---19.36 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01298
X-RAY DIFFRACTIONr_bond_other_d0.0110.01780
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.739134
X-RAY DIFFRACTIONr_angle_other_deg1.3941.624184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.874510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.37726.6676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg3.0841512
X-RAY DIFFRACTIONr_chiral_restr0.0390.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116
X-RAY DIFFRACTIONr_gen_planes_other00.0220
LS refinement shellResolution: 1.601→1.643 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 6 -
Rwork0.29 54 -
all-60 -
obs--77.92 %

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