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- PDB-4af9: Crystal Structure of Epithelial Adhesin 1 A domain (Epa1A) from C... -

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Basic information

Entry
Database: PDB / ID: 4af9
TitleCrystal Structure of Epithelial Adhesin 1 A domain (Epa1A) from Candida glabrata in complex with Galb1-3Glc
ComponentsEPA1P
KeywordsCELL ADHESION / LECTIN / TISSUE INVASION / PATHOGENICITY
Function / homology
Function and homology information


GLEYA adhesin domain / GLEYA domain / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Epa1p
Similarity search - Component
Biological speciesCANDIDA GLABRATA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMaestre-Reyna, M. / Diderrich, R. / Veelders, M.S. / Eulenburg, G. / Kalugin, V. / Brueckner, S. / Keller, P. / Rupp, S. / Moesch, H.-U. / Essen, L.-O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for Promiscuity and Specificity During Candida Glabrata Invasion of Host Epithelia.
Authors: Maestre-Reyna, M. / Diderrich, R. / Veelders, M.S. / Eulenburg, G. / Kalugin, V. / Bruckner, S. / Keller, P. / Rupp, S. / Mosch, H. / Essen, L.
History
DepositionJan 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Jul 1, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_special_symmetry / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: EPA1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2017
Polymers29,4371
Non-polymers7656
Water4,882271
1
A: EPA1P
hetero molecules

A: EPA1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,40314
Polymers58,8732
Non-polymers1,53012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4820 Å2
ΔGint-24.1 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.640, 104.330, 69.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2093-

HOH

21A-2141-

HOH

31A-2234-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein EPA1P / EPITHELIAL ADHESIN 1


Mass: 29436.619 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 31-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Strain: CBS138 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: Q6VBJ0
#2: Polysaccharide beta-D-galactopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 276 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsB-D-GALACTOSE (GAL): BUILDS GALB1-3GLC WITH GLUCOSE. ALPHA-D-GLUCOSE (GLC): BUILDS GALB1-3GLC WITH ...B-D-GALACTOSE (GAL): BUILDS GALB1-3GLC WITH GLUCOSE. ALPHA-D-GLUCOSE (GLC): BUILDS GALB1-3GLC WITH GALACTOSE. IS A MIXTURE OF ALPHA AND BETA GLUCOSE
Sequence detailsWE WORKED WITH THE N-TERMINAL ADHESIVE DOMAIN OF EPA1A, WHILE Q6VBJ0 PRESENTS THE ENTIRE SEQUENCE. ...WE WORKED WITH THE N-TERMINAL ADHESIVE DOMAIN OF EPA1A, WHILE Q6VBJ0 PRESENTS THE ENTIRE SEQUENCE. WE USED Q6VBJ0 SEQUENCE NUMBERING THROUGHOUT THE PRESENT WORK.

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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: 2.31 Å3/Da / Density % sol: 46.75 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 0.025 M LACTOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 24, 2009 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DIAMOND AND GE FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→19.89 Å / Num. obs: 43249 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJP

2xjp


Resolution: 1.5→19.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.557 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18576 1498 3.5 %RANDOM
Rwork0.15579 ---
obs0.15683 41751 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 61 271 2141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222064
X-RAY DIFFRACTIONr_bond_other_d0.0010.021397
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9792837
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0023413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83323.51194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96215306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.267158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212319
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02455
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_it1.60431219
X-RAY DIFFRACTIONr_mcbond_other0.5443484
X-RAY DIFFRACTIONr_mcangle_it2.46741987
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1273845
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1144831
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 111 -
Rwork0.259 3023 -
obs--98.4 %
Refinement TLS params.Method: refined / Origin x: 35.981 Å / Origin y: 16.536 Å / Origin z: 1.805 Å
111213212223313233
T0.0232 Å20.002 Å20.0072 Å2-0.0092 Å2-0.0066 Å2--0.0171 Å2
L0.9876 °2-0.2594 °20.2252 °2-0.5502 °2-0.3078 °2--0.7513 °2
S-0.0249 Å °-0.0192 Å °-0.0472 Å °0.0012 Å °0.0325 Å °0.0161 Å °-0.0076 Å °-0.0558 Å °-0.0076 Å °

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