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

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Entry
Database: PDB / ID: 4coz
TitleCrystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Galb1-3GlcNAc
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: 2.3 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPITHELIAL ADHESIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5135
Polymers29,9381
Non-polymers5754
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.280, 61.260, 106.620
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: 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-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 181 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.: 178 / 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: 2.25 Å3/Da / Density % sol: 45.41 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.08 M SODIUM ACETATE PH4.6, 1.6 M AMMONIUM SULFATE, 20% GLYCEROL, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALB1-3GLCNAC

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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 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 2.25→53.12 Å / Num. obs: 13420 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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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: 2.3→53.17 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.984 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22029 624 5 %RANDOM
Rwork0.17779 ---
obs0.17994 11930 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 37 178 2006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021893
X-RAY DIFFRACTIONr_bond_other_d0.0020.021639
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9682584
X-RAY DIFFRACTIONr_angle_other_deg0.7833.0033769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77224.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8915262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.466156
X-RAY DIFFRACTIONr_chiral_restr0.070.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
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_it0.9031.076906
X-RAY DIFFRACTIONr_mcbond_other0.91.072904
X-RAY DIFFRACTIONr_mcangle_it1.7061.6061130
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5571.101987
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 35 -
Rwork0.221 866 -
obs--99.89 %
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)
10.15390.4464-0.78061.3578-2.34554.1214-0.08280.0194-0.0038-0.2397-0.0224-0.08090.3381-0.00410.10510.14530.01280.00480.1160.04540.13594.999-4.586122.9455
24.01971.6998-3.29371.4189-1.52942.74510.01310.61620.48840.15030.2829-0.07670.0145-0.4806-0.2960.12110.0211-0.00690.2110.12140.2199-0.66323.8078106.4432
31.1862-0.4103-0.53280.7977-0.71891.48690.01070.0681-0.0071-0.0032-0.0193-0.0080.0126-0.03790.00860.0938-0.0119-0.01260.10830.00680.10666.176913.0585113.9824
41.17611.5557-1.13292.1478-1.28811.6272-0.0204-0.0459-0.04240.0166-0.0097-0.0450.05760.20620.03010.13430.02050.00550.16590.03210.114910.66238.2575118.0707
50.19690.3773-0.26590.945-0.95791.28170.0144-0.04090.0634-0.0024-0.01490.08650.0887-0.07250.00040.1437-0.00050.02660.12920.01540.0988-1.86370.7139123.7805
60.6774-0.76721.11384.9501-3.86763.49980.0558-0.1174-0.0285-0.00830.30860.54140.084-0.3047-0.36440.1560.02610.06880.12350.05860.0953-4.87377.7058128.9819
70.15070.5179-0.41042.0596-1.36741.37340.0170.00560.03030.04670.0163-0.00110.01220.1459-0.03320.13270.01720.03340.14610.00250.10762.43099.037123.808
81.37392.55730.36037.04612.95572.50830.2242-0.3371-0.11490.4264-0.4271-0.10350.18020.17930.20290.15990.02690.0220.15130.08660.15797.86180.3101131.5423
91.5032.2928-4.51773.5039-6.906313.626-0.16650.0064-0.0817-0.1743-0.0285-0.11460.2972-0.02390.1950.3180.01190.06470.0863-0.02050.0223-1.7258-16.4809125.8931
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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