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- PDB-7o9o: Crystal structure of the Awp3b (adhesin-like wall protein 3b) A-d... -

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Basic information

Entry
Database: PDB / ID: 7o9o
TitleCrystal structure of the Awp3b (adhesin-like wall protein 3b) A-domain from Candida glabrata
ComponentsAWP3b
KeywordsCELL ADHESION / Candida glabrata / putative adhesin / adhesin-like wall protein / Awp / adhesion / beta-helix / haze-protective factor / cell wall protein
Function / homologyAWP3b
Function and homology information
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AWP3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7723
Polymers38,7131
Non-polymers582
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-15 kcal/mol
Surface area13960 Å2
Unit cell
Length a, b, c (Å)147.970, 147.970, 117.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-998-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium phosphate, 0.1 M potassium phosphate, 0.1 M MES pH6.5, 2.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→56.28 Å / Num. obs: 69278 / % possible obs: 96.96 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.75 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.68
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 6889 / CC1/2: 0.431 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Awp3bA-Gd

Resolution: 1.55→56.28 Å / SU ML: 0.1933 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.88 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1882 6595 5 %
Rwork0.1593 125200 -
obs0.1608 69278 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.78 Å2
Refinement stepCycle: LAST / Resolution: 1.55→56.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 2 571 3061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822601
X-RAY DIFFRACTIONf_angle_d0.99193547
X-RAY DIFFRACTIONf_chiral_restr0.0683393
X-RAY DIFFRACTIONf_plane_restr0.0064479
X-RAY DIFFRACTIONf_dihedral_angle_d15.18091534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.32462300.32464158X-RAY DIFFRACTION93.94
1.57-1.590.34432190.32044128X-RAY DIFFRACTION94.42
1.59-1.610.31552270.31414174X-RAY DIFFRACTION94.24
1.61-1.630.31362420.29714185X-RAY DIFFRACTION94.55
1.63-1.650.30612230.2993970X-RAY DIFFRACTION90.15
1.65-1.670.28612220.28613791X-RAY DIFFRACTION86.75
1.67-1.690.28652220.27064081X-RAY DIFFRACTION93.62
1.69-1.720.28942040.26534274X-RAY DIFFRACTION94.63
1.72-1.750.25972070.24724179X-RAY DIFFRACTION94.83
1.75-1.770.20341890.23344266X-RAY DIFFRACTION95.21
1.77-1.80.25162460.22774149X-RAY DIFFRACTION94.68
1.8-1.840.2742190.21514183X-RAY DIFFRACTION94.95
1.84-1.870.20742050.19664264X-RAY DIFFRACTION95.02
1.87-1.910.23122360.18654168X-RAY DIFFRACTION95.12
1.91-1.950.19711930.16824158X-RAY DIFFRACTION93.85
1.95-20.20181930.16163853X-RAY DIFFRACTION86.45
2-2.050.18562140.15714252X-RAY DIFFRACTION96.5
2.05-2.10.17742210.15394243X-RAY DIFFRACTION96.02
2.1-2.170.21191910.14434240X-RAY DIFFRACTION95.74
2.17-2.240.15942250.13474314X-RAY DIFFRACTION96.35
2.24-2.320.15622400.13044228X-RAY DIFFRACTION97.02
2.32-2.410.18992130.12714337X-RAY DIFFRACTION97.47
2.41-2.520.16152260.1384023X-RAY DIFFRACTION91.16
2.52-2.650.1962230.15484079X-RAY DIFFRACTION92.72
2.65-2.820.17942000.15244364X-RAY DIFFRACTION97.79
2.82-3.030.20042370.15064318X-RAY DIFFRACTION97.89
3.03-3.340.17052570.13414303X-RAY DIFFRACTION98.45
3.34-3.820.13692260.11143980X-RAY DIFFRACTION89.99
3.82-4.820.11562420.10264320X-RAY DIFFRACTION98.38
4.82-56.280.21922030.17094218X-RAY DIFFRACTION94.47
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)
10.176184621513-0.1585161368030.183385819880.363047644075-0.1209211700630.776831429176-0.009706494142740.0783376671127-0.00397880766184-0.197214742006-0.03331869225770.0456127208019-0.04376572882120.0597814633797-2.79035300441E-50.236200662804-0.0162076830764-0.009067647833290.1464260254770.03246181720840.159952160753105.870537206157.440451662-15.8352601107
20.1470888082420.05803219291540.109931078680.935372302377-0.07791240923540.7447293581980.002100842387580.03306277839510.0186630992975-0.0874788688977-0.01630827343240.137692161490.05972351973930.04285674971220.0007621933284510.1447877457470.00191072225442-0.003631068991520.1181174654020.01376401307250.15232820779103.348893611146.1443624672.15704837345
30.4219441044930.1460119022940.3578729641640.3537761400460.07904597687480.3100981093710.0114061007951-0.119040278447-0.02593612666310.0978167238843-0.0431585447630.1478782502610.198676058584-0.0716164857125-3.52264811543E-50.223483249857-0.01589890017670.05245598789050.1523983842950.006768588659640.19155364242996.6497131026136.67815700220.1650300823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 281 )
3X-RAY DIFFRACTION3chain 'A' and (resid 282 through 344)

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