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- PDB-4afb: Crystal Structure of subtype-switched Epithelial Adhesin 1 to 3 A... -

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Basic information

Entry
Database: PDB / ID: 4afb
TitleCrystal Structure of subtype-switched Epithelial Adhesin 1 to 3 A domain (Epa1to3A) from Candida glabrata in complex with glycerol
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
Biological speciesCANDIDA GLABRATA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,6956
Polymers29,2871
Non-polymers4085
Water2,936163
1
A: EPA1P
hetero molecules

A: EPA1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,39012
Polymers58,5732
Non-polymers81710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3420 Å2
ΔGint-38.6 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.740, 103.530, 70.480
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-2001-

HOH

21A-2047-

HOH

31A-2138-

HOH

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Components

#1: Protein EPA1P / EPITHELIAL ADHESIN 1


Mass: 29286.525 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 31-271 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SUB-TYPE SWITCHED EPA1A VARIANT WHICH EMULATES THE BINDING POCKET OF EPA3A
Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Strain: CBS138 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: Q6VBJ0
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 226 TO ILE ENGINEERED RESIDUE IN CHAIN A, GLU 227 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, ARG 226 TO ILE ENGINEERED RESIDUE IN CHAIN A, GLU 227 TO GLY ENGINEERED RESIDUE IN CHAIN A, TYR 228 TO LYS
Sequence detailsEPA1A REPRESENTS ONLY THE SIGNAL PEPTIDE FREE N-TERMINAL REGION FROM THE Q6VBJ0. WE USED THE Q6VBJ0 ...EPA1A REPRESENTS ONLY THE SIGNAL PEPTIDE FREE N-TERMINAL REGION FROM THE Q6VBJ0. WE USED THE Q6VBJ0 NUMBERING THROUGHOUT OUR 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: 2.36 Å3/Da / Density % sol: 47.89 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2010 / Details: FOCUSING MIRRORS
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→46.18 Å / Num. obs: 22061 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 21.39 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EPA1A WILD TYPE

Resolution: 1.9→37.87 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 782 3.5 %
Rwork0.1675 --
obs0.1693 22056 99.38 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.809 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 26.01 Å2
Baniso -1Baniso -2Baniso -3
1--4.2366 Å20 Å20 Å2
2--6.8502 Å20 Å2
3----2.6136 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 25 163 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141918
X-RAY DIFFRACTIONf_angle_d1.2752623
X-RAY DIFFRACTIONf_dihedral_angle_d11.744674
X-RAY DIFFRACTIONf_chiral_restr0.088266
X-RAY DIFFRACTIONf_plane_restr0.006338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.01910.32341390.22963464X-RAY DIFFRACTION99
2.0191-2.1750.26831190.17433520X-RAY DIFFRACTION100
2.175-2.39380.20631340.16123532X-RAY DIFFRACTION100
2.3938-2.74010.23461170.15693544X-RAY DIFFRACTION100
2.7401-3.45190.23251300.15793572X-RAY DIFFRACTION99
3.4519-37.87750.17561430.16523642X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 1.4539 Å / Origin y: 35.4497 Å / Origin z: 1.6428 Å
111213212223313233
T0.095 Å2-0.0074 Å2-0.0246 Å2-0.0781 Å20.012 Å2--0.089 Å2
L1.625 °2-0.1264 °2-0.4141 °2-0.879 °20.2496 °2--1.6458 °2
S-0.0026 Å °0.046 Å °0.1794 Å °0.0171 Å °0.017 Å °-0.0013 Å °-0.0962 Å °0.0813 Å °0.0037 Å °
Refinement TLS groupSelection details: CHAIN A AND (RESSEQ 40:266)

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