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- PDB-4cou: Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from C... -

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Basic information

Entry
Database: PDB / ID: 4cou
TitleCrystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Lactose
ComponentsEPITHELIAL ADHESIN 6
KeywordsCELL ADHESION / LECTIN / TISSUE INVASION / PATHOGENICITY
Function / homology
Function and homology information


cell-abiotic substrate adhesion / single-species biofilm formation on inanimate substrate / fungal biofilm matrix / adhesion of symbiont to host / fungal-type cell wall / carbohydrate binding / cell surface / extracellular region / metal ion binding
Similarity search - Function
GLEYA adhesin domain / GLEYA domain / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-lactose / ACETATE ION / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesCANDIDA GLABRATA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKock, M. / Maestre-Reyna, M. / Diderrich, R. / Moesch, H.-U. / Essen, L.-O.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Hotspots Determine Functional Diversity of the Candida Glabrata Epithelial Adhesin Family
Authors: Diderrich, R. / Kock, M. / Maestre-Reyna, M. / Rupp, S. / Essen, L.-O. / Moesch, H.-U.
History
DepositionJan 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 8, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.5May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPITHELIAL ADHESIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4715
Polymers29,9381
Non-polymers5344
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.300, 61.100, 106.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein EPITHELIAL ADHESIN 6


Mass: 29937.945 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 26-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Strain: CBS138 / Plasmid: PET28A / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: Q6FX55
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 248 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.14 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.08 M SODIUM ACETATE PH:4.6, 1.6 M AMMONIUM SULFATE, 20% GLYCEROL, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH MARMOSAIC 255 MM / Detector: CCD / Date: Sep 16, 2012
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.48→28.77 Å / Num. obs: 45573 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.1
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRUNED VERSION OF PDB ENTRY 4AF9

4af9


Resolution: 1.48→26.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.189 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17152 1173 2.6 %RANDOM
Rwork0.14427 ---
obs0.145 44337 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.48→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 34 245 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021922
X-RAY DIFFRACTIONr_bond_other_d0.0010.021642
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9672640
X-RAY DIFFRACTIONr_angle_other_deg0.7363.0033796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3224.45792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64715259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.761155
X-RAY DIFFRACTIONr_chiral_restr0.0730.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
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_it1.7571.75936
X-RAY DIFFRACTIONr_mcbond_other1.7131.746934
X-RAY DIFFRACTIONr_mcangle_it2.1332.6271173
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0571.888986
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_restr2.21133564
X-RAY DIFFRACTIONr_sphericity_free30.6785100
X-RAY DIFFRACTIONr_sphericity_bonded8.65653651
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 79 -
Rwork0.239 3234 -
obs--99.94 %

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