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- PDB-2y7m: Structure of N-terminal domain of Candida albicans als9-2 (Pt der... -

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Basic information

Entry
Database: PDB / ID: 2y7m
TitleStructure of N-terminal domain of Candida albicans als9-2 (Pt derivative)
ComponentsAGGLUTININ-LIKE ALS9 PROTEIN
KeywordsCELL ADHESION / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


cell adhesion involved in multi-species biofilm formation / fungal-type cell wall / cell adhesion involved in single-species biofilm formation / side of membrane / cell adhesion molecule binding / cell-cell adhesion / cell adhesion / 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 / 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 / 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 / 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 / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Agglutinin-like protein 9 / :
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.98 Å
AuthorsSalgado, P.S. / Cota, E.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / 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
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ-LIKE ALS9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,5741
Polymers33,5741
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.723, 68.717, 120.017
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 ALS9 PROTEIN / NT_ALS9-2


Mass: 33573.992 Da / Num. of mol.: 1 / Fragment: N-TERMINAL, RESIDUES 18-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: PET32 XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI / References: UniProt: Q5A8T1, UniProt: A0A1D8PQ86*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE EXCLUDES N-TERMINAL SIGNAL SEQUENCE (18 RESIDUES)

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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: 49 % / Description: PT WAS USED AS ANOMALOUS SCATTERER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.068
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.068 Å / Relative weight: 1
ReflectionResolution: 1.83→68.9 Å / Num. obs: 26698 / % possible obs: 99.7 % / Observed criterion σ(I): 5.6 / Redundancy: 13.7 % / Biso Wilson estimate: 26.401 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.9
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.98→19.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.425 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.183
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25993 1063 5.1 %RANDOM
Rwork0.20574 ---
obs0.20852 19626 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 0 107 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9333200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7452592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.528154
X-RAY DIFFRACTIONr_chiral_restr0.1270.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211765
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_it1.1241.51490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82522436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8893846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.24.5764
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: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 82 -
Rwork0.226 1418 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 30.5267 Å / Origin y: 57.8584 Å / Origin z: 16.5126 Å
111213212223313233
T0.0086 Å2-0.0048 Å2-0.0033 Å2-0.0371 Å2-0.0109 Å2--0.0065 Å2
L0.3124 °2-0.0272 °2-0.0018 °2-2.2233 °2-1.0741 °2--0.8768 °2
S0.0106 Å °0.0329 Å °-0.0213 Å °-0.0745 Å °0.0265 Å °0.061 Å °0.0808 Å °-0.0411 Å °-0.037 Å °

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