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

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Entry
Database: PDB / ID: 4cov
TitleCrystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Gala1-3Gal
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
ACETATE ION / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesCANDIDA GLABRATA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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 / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / 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.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,3794
Polymers29,9381
Non-polymers4413
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.520, 63.290, 110.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: CBS 138 / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: Q6FX55
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.23 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.01 M SODIUM ACETATE PH 4.6, 30% PEG4000, 0.2 M AMMONIUM ACETATE, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALA1-3GAL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2013
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.5→41.58 Å / Num. obs: 47367 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % 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: 1.5→41.58 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.425 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17661 1223 2.6 %RANDOM
Rwork0.14965 ---
obs0.15034 46100 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 28 339 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021945
X-RAY DIFFRACTIONr_bond_other_d0.0010.021687
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9622674
X-RAY DIFFRACTIONr_angle_other_deg0.7183.0033892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36224.36294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07915271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.011155
X-RAY DIFFRACTIONr_chiral_restr0.0740.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
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_it1.351.78933
X-RAY DIFFRACTIONr_mcbond_other1.3141.779931
X-RAY DIFFRACTIONr_mcangle_it1.6982.6731167
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5161.9811012
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_restr1.14133632
X-RAY DIFFRACTIONr_sphericity_free35.138578
X-RAY DIFFRACTIONr_sphericity_bonded10.13353828
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 83 -
Rwork0.247 3377 -
obs--99.51 %

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