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- PDB-6y98: Crystal Structure of subtype-switched Epithelial Adhesin 9 to 1 A... -

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Basic information

Entry
Database: PDB / ID: 6y98
TitleCrystal Structure of subtype-switched Epithelial Adhesin 9 to 1 A domain (Epa9-CBL2Epa1) from Candida glabrata in complex with beta-lactose
ComponentsPA14 domain-containing protein
KeywordsCELL ADHESION / Epithelial Adhesin
Function / homologyGLEYA adhesin domain / GLEYA domain / PA14/GLEYA domain / PA14 domain profile. / metal ion binding / beta-lactose / Candida glabrata strain CBS138 chromosome A complete sequence
Function and homology information
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsHoffmann, D. / Diderrich, R. / Kock, M. / Friederichs, S. / Reithofer, V. / Essen, L.-O. / Moesch, H.-U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Functional reprogramming ofCandida glabrataepithelial adhesins: the role of conserved and variable structural motifs in ligand binding.
Authors: Hoffmann, D. / Diderrich, R. / Reithofer, V. / Friederichs, S. / Kock, M. / Essen, L.O. / Mosch, H.U.
History
DepositionMar 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / citation_author / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / 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.id / _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 / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _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_comp_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: PA14 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6143
Polymers33,2311
Non-polymers3822
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-11 kcal/mol
Surface area10810 Å2
Unit cell
Length a, b, c (Å)65.289, 65.289, 121.877
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein PA14 domain-containing protein


Mass: 33231.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: EPA9, CAGL0A01366g / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B4UMX2
#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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium Sodium tartrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.8→41.45 Å / Num. obs: 15594 / % possible obs: 99.5 % / Redundancy: 9.6 % / Biso Wilson estimate: 93.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Net I/σ(I): 18.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.4 / Num. unique obs: 1132 / CC1/2: 0.769 / Rpim(I) all: 0.475 / Rrim(I) all: 1.48 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CP0

4cp0


Resolution: 2.8→40.63 Å / SU ML: 0.4319 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.7319 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 806 5.66 %
Rwork0.2037 13431 -
obs0.2062 14237 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 24 0 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511932
X-RAY DIFFRACTIONf_angle_d1.07362634
X-RAY DIFFRACTIONf_chiral_restr0.0661255
X-RAY DIFFRACTIONf_plane_restr0.0068346
X-RAY DIFFRACTIONf_dihedral_angle_d11.25941106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.41641460.33812283X-RAY DIFFRACTION99.79
2.98-3.210.33851590.27962196X-RAY DIFFRACTION100
3.21-3.530.2821020.24562288X-RAY DIFFRACTION100
3.53-4.040.24591700.2112194X-RAY DIFFRACTION99.2
4.04-5.090.17561140.16492263X-RAY DIFFRACTION99.96
5.09-40.630.25421150.19312207X-RAY DIFFRACTION97.2
Refinement TLS params.Method: refined / Origin x: -6.85327035664 Å / Origin y: 23.379755929 Å / Origin z: 5.39580819428 Å
111213212223313233
T0.865811535189 Å20.362635456561 Å2-0.165279587043 Å2-0.989289711459 Å20.281517805475 Å2--1.37624330653 Å2
L3.19398033933 °2-0.162963664173 °2-2.40522028367 °2-3.8952308265 °20.530866563308 °2--3.01537437959 °2
S0.426056286512 Å °0.958506566543 Å °0.981173469681 Å °-0.103637962889 Å °-0.0753155579179 Å °0.360612692582 Å °-0.776813917641 Å °-0.617954828017 Å °-0.187545431238 Å °
Refinement TLS groupSelection details: all

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