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- PDB-6rhb: Crystal structure of the amyloid-like IATLYV segment from the Can... -

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Basic information

Entry
Database: PDB / ID: 6rhb
TitleCrystal structure of the amyloid-like IATLYV segment from the Candida albicans Agglutinin-like protein (Adhesin) 5
ComponentsAgglutinin-like protein 5
KeywordsPROTEIN FIBRIL / amyloid fibril from Candida albicans
Function / homology
Function and homology information


biological process involved in symbiotic interaction / side of membrane / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Cell-wall agglutinin N-terminal ligand-sugar binding / Cell-wall agglutinin N-terminal ligand-sugar binding / 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: 1.26 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Agglutinin-like protein 5


Theoretical massNumber of molelcules
Total (without water)6791
Polymers6791
Non-polymers00
Water181
1
B: Agglutinin-like protein 5
x 36


Theoretical massNumber of molelcules
Total (without water)24,43736
Polymers24,43736
Non-polymers00
Water64936
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
crystal symmetry operation2_154-x-7/2,-y,z-1/21
crystal symmetry operation2_254-x-5/2,-y,z-1/21
crystal symmetry operation2_354-x-3/2,-y,z-1/21
crystal symmetry operation2_454-x-1/2,-y,z-1/21
crystal symmetry operation2_554-x+1/2,-y,z-1/21
crystal symmetry operation2_654-x+3/2,-y,z-1/21
crystal symmetry operation2_754-x+5/2,-y,z-1/21
crystal symmetry operation2_854-x+7/2,-y,z-1/21
crystal symmetry operation2_954-x+9/2,-y,z-1/21
crystal symmetry operation3_144-x-4,y-1/2,-z-1/21
crystal symmetry operation3_244-x-3,y-1/2,-z-1/21
crystal symmetry operation3_344-x-2,y-1/2,-z-1/21
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
crystal symmetry operation3_544-x,y-1/2,-z-1/21
crystal symmetry operation3_644-x+1,y-1/2,-z-1/21
crystal symmetry operation3_744-x+2,y-1/2,-z-1/21
crystal symmetry operation3_844-x+3,y-1/2,-z-1/21
crystal symmetry operation3_944-x+4,y-1/2,-z-1/21
crystal symmetry operation4_155x-7/2,-y+1/2,-z1
crystal symmetry operation4_255x-5/2,-y+1/2,-z1
crystal symmetry operation4_355x-3/2,-y+1/2,-z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation4_655x+3/2,-y+1/2,-z1
crystal symmetry operation4_755x+5/2,-y+1/2,-z1
crystal symmetry operation4_855x+7/2,-y+1/2,-z1
crystal symmetry operation4_955x+9/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)9.490, 17.870, 22.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 678.817 Da / Num. of mol.: 1
Fragment: Amyloid spine segment IATLYV from Als5 (residues 196-201) secreted by Candida albicans
Source method: obtained synthetically / Details: IATLYV from Als5, synthesized / Source: (synth.) Candida albicans (yeast) / References: UniProt: O13368
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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
Details: Reservoir contained 0.1M tri-Sodium citrate pH 5.6, 1.0M Ammonium phosphate

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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: Sep 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.26→13.97 Å / Num. obs: 1076 / % possible obs: 91.1 % / Redundancy: 11.539 % / Biso Wilson estimate: 11.103 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.246 / Rrim(I) all: 0.258 / Χ2: 0.749 / Net I/σ(I): 6.8 / Num. measured all: 12416
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
1.26-1.3210.9330.7572.89984153900.9710.79558.8
1.32-1.3911.3310.822.7814731411300.890.85992.2
1.39-1.4811.9490.7473.3516251361360.9380.78100
1.48-1.5812.2390.524.7114321341170.9160.54287.3
1.58-1.7111.6870.5384.4113441161150.870.56499.1
1.71-1.8712.4470.317.5714191181140.9620.32396.6
1.87-2.0912.1180.2228.67112797930.9950.23295.9
2.09-2.4110.670.18110.351035101970.9810.19296
2.41-2.9611.2470.16111.9186677770.9940.169100
2.96-4.1810.7270.1214.6370866660.9980.126100
4.18-13.979.8290.10915.2240342410.9970.11597.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.3 Å13.97 Å
Translation1.3 Å13.97 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: 1.26→13.97 Å / Cor.coef. Fo:Fc: 0.99 / Cor.coef. Fo:Fc free: 0.992 / SU B: 1.303 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.031
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1039 108 10 %RANDOM
Rwork0.0997 ---
obs0.1002 968 91.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 8.2 Å2 / Biso mean: 4.607 Å2 / Biso min: 3.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.26→13.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48 0 0 1 49
Biso mean---7.22 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01348
X-RAY DIFFRACTIONr_bond_other_d0.0070.01752
X-RAY DIFFRACTIONr_angle_refined_deg1.561.69366
X-RAY DIFFRACTIONr_angle_other_deg1.2731.598117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.833201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.052157
X-RAY DIFFRACTIONr_chiral_restr0.0770.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0251
X-RAY DIFFRACTIONr_gen_planes_other00.029
X-RAY DIFFRACTIONr_rigid_bond_restr0.4553100
LS refinement shellResolution: 1.26→1.407 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.241 24 -
Rwork0.175 218 -
all-242 -
obs--76.58 %

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