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

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Entry
Database: PDB / ID: 4cow
TitleCrystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with the T-antigen (Galb1-3GalNAc)
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: 2.15 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: Data collection / Database references
Revision 1.2Jul 8, 2015Group: Data collection / Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6May 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 / chem_comp ...atom_site / 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 / _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 6, 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)30,6056
Polymers29,9381
Non-polymers6675
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.350, 61.100, 106.610
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 26-471
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 beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 204 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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.36 % / 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, SOAKED WITH GALB1-3GALNAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 2→34.24 Å / Num. obs: 18879 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7

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Processing

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

4af9


Resolution: 2.15→32.69 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.713 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 740 4.8 %RANDOM
Rwork0.17699 ---
obs0.17963 14534 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 43 200 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021914
X-RAY DIFFRACTIONr_bond_other_d0.0010.021668
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9712612
X-RAY DIFFRACTIONr_angle_other_deg0.763.0033846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07724.36294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96715270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.833156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
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_it1.161.315910
X-RAY DIFFRACTIONr_mcbond_other1.1571.31908
X-RAY DIFFRACTIONr_mcangle_it2.1451.9611136
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9541.4121004
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 36 -
Rwork0.214 1066 -
obs--99.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24040.5687-0.31711.8268-1.96853.64190.0040.024-0.0319-0.0478-0.0151-0.10760.1080.05110.01110.05890.05510.04110.0690.05330.11214.945-4.847127.043
26.86061.7525-2.52790.93-1.47152.37340.28670.19510.76550.05740.05380.1914-0.0601-0.1713-0.34060.0579-0.0018-0.00560.16310.10870.1732-0.64124.737109.413
31.2788-0.4985-0.23360.7085-0.7761.5144-0.0285-0.01550.02480.05410.0209-0.0224-0.0491-0.01340.00760.0666-0.0103-0.00380.06540.01430.07216.15913.481117.824
41.03441.2251-0.99952.0209-1.12011.2965-0.0363-0.0433-0.07510.1436-0.0339-0.1230.02310.21250.07030.10460.0258-0.00820.13230.02760.070710.6718.439122.04
50.23320.4866-0.64211.0322-1.27672.01040.0343-0.0260.04180.1074-0.08110.12550.0345-0.010.04670.1285-0.03270.08480.0948-0.02450.1394-1.8930.636127.963
61.1586-0.53821.20242.7282-1.88562.2314-0.0129-0.18260.07920.25860.24560.5128-0.0319-0.3998-0.23270.14890.01590.08050.12730.05340.1428-4.8867.858133.384
70.23730.4723-0.3531.6326-1.06631.11940.0135-0.01550.03930.19870.0026-0.0088-0.07480.066-0.01610.15210.02920.02490.07420.01160.08452.439.232128.037
81.23522.44530.48896.4854.15276.47490.2941-0.4784-0.19060.6549-0.7328-0.12980.42520.21680.43870.1834-0.0707-0.01250.21740.10030.08287.790.132135.996
91.46010.9352-4.67896.536-5.839616.3624-0.02220.043-0.19380.1261-0.6198-0.211-0.07440.1720.6420.3107-0.04630.06550.0729-0.00320.0411-1.717-17.23130.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 67
2X-RAY DIFFRACTION2A68 - 81
3X-RAY DIFFRACTION3A82 - 127
4X-RAY DIFFRACTION4A128 - 150
5X-RAY DIFFRACTION5A151 - 193
6X-RAY DIFFRACTION6A194 - 215
7X-RAY DIFFRACTION7A216 - 238
8X-RAY DIFFRACTION8A239 - 258
9X-RAY DIFFRACTION9A259 - 268

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