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- PDB-7o9p: Crystal structure of the Awp3b (adhesin-like wall protein 3b) A-d... -

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Basic information

Entry
Database: PDB / ID: 7o9p
TitleCrystal structure of the Awp3b (adhesin-like wall protein 3b) A-domain from Candida glabrata showing a gadolinium cluster
ComponentsAWP3b
KeywordsCELL ADHESION / Candida glabrata / adhesion / adhesin / Awp / adhesin-like wall protein / gadolinium / gadolinium cluster / lanthanide / lanthanide cluster / haze-protective factors / beta-helix
Function / homologyGADOLINIUM ATOM / AWP3b
Function and homology information
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsReithofer, V. / de Groot, P. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Plos Pathog. / Year: 2021
Title: A novel class of Candida glabrata cell wall proteins with beta-helix fold mediates adhesion in clinical isolates.
Authors: Reithofer, V. / Fernandez-Pereira, J. / Alvarado, M. / de Groot, P. / Essen, L.O.
History
DepositionApr 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AWP3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,31843
Polymers38,7131
Non-polymers6,60542
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12940 Å2
Unit cell
Length a, b, c (Å)144.397, 144.397, 113.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

21A-768-

HOH

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Components

#1: Protein AWP3b


Mass: 38713.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: AWP3b, GWK60_J11715 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G7JIM8
#2: Chemical...
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: Gd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 7.0, 3.0 M sodium chloride crystals soaked with 50 mM gadolinium (III) acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.71237 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71237 Å / Relative weight: 1
ReflectionResolution: 1.99→84.2 Å / Num. obs: 30650 / % possible obs: 99.8 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.025 / Rrim(I) all: 0.107 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0516.40.5493664322290.8070.1380.5674.999.4
8.94-84.2200.06777343870.9950.0160.06961.2100

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
CRANK2phasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.99→27.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.24 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1508 4.8 %RANDOM
Rwork0.1685 ---
obs0.1705 29914 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.06 Å2 / Biso mean: 32.892 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å2-0 Å2
2--0.47 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: final / Resolution: 1.99→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 41 290 2640
Biso mean--98.64 47.08 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132416
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172060
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6343225
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5684803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6885308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.07225.217115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33215363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.47155
X-RAY DIFFRACTIONr_chiral_restr0.0740.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02480
LS refinement shellResolution: 1.99→2.04 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.283 110 -
Rwork0.232 2201 -
obs--99.91 %

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