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- PDB-7o9q: Crystal structure of the Awp1 (adhesin-like wall protein 1) A-dom... -

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Basic information

Entry
Database: PDB / ID: 7o9q
TitleCrystal structure of the Awp1 (adhesin-like wall protein 1) A-domain from Candida glabrata
ComponentsAwp1A
KeywordsCELL ADHESION / Candida glabrata / adhesin / adhesion / Awp / adhesin-like wall protein / beta-helix / haze-protective factor
Function / homologyfungal-type cell wall / Trimeric LpxA-like superfamily / pentane-1,5-diol / Uncharacterized protein
Function and homology information
Biological species[Candida] glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Awp1A
B: Awp1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7596
Polymers71,3432
Non-polymers4174
Water12,034668
1
A: Awp1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7752
Polymers35,6711
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Awp1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9844
Polymers35,6711
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.280, 83.280, 274.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Awp1A


Mass: 35671.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata (fungus) / Gene: AWP1, CAGL0J02508g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FPN0
#2: Chemical
ChemComp-9JE / pentane-1,5-diol / Pentane-1,5-diol


Mass: 104.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPSO/Bis-Tris pH 6.5, 10% (w/v) PEG 8000, 20% 1,5-pentanediol, 0.5 mM erbium (III) chloride, 0.5 mM terbium (III) chloride, 0.5 mM ytterbium (III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 1.85→45.81 Å / Num. obs: 83156 / % possible obs: 99.16 % / Redundancy: 2 % / Biso Wilson estimate: 33.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.64
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 1.62 / Num. unique obs: 8101 / CC1/2: 0.95

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Processing

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

Resolution: 1.85→45.81 Å / SU ML: 0.2762 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.839 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 1621 1.96 %
Rwork0.1871 81113 -
obs0.1875 82734 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 28 668 5218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394671
X-RAY DIFFRACTIONf_angle_d0.67366402
X-RAY DIFFRACTIONf_chiral_restr0.0515805
X-RAY DIFFRACTIONf_plane_restr0.0039826
X-RAY DIFFRACTIONf_dihedral_angle_d10.90132753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.48051320.41356509X-RAY DIFFRACTION97.53
1.9-1.970.34671240.32756609X-RAY DIFFRACTION98.35
1.97-2.040.31941180.28176644X-RAY DIFFRACTION98.99
2.04-2.120.26991230.24976674X-RAY DIFFRACTION99.26
2.12-2.210.2621320.22986688X-RAY DIFFRACTION99.4
2.21-2.330.25881260.20626758X-RAY DIFFRACTION99.7
2.33-2.480.21071380.18976722X-RAY DIFFRACTION99.59
2.48-2.670.17951490.17966751X-RAY DIFFRACTION99.6
2.67-2.940.19361330.17556787X-RAY DIFFRACTION99.51
2.94-3.360.22961300.17176857X-RAY DIFFRACTION99.66
3.36-4.230.18771630.15826903X-RAY DIFFRACTION99.61
4.23-49.510.16881530.17267211X-RAY DIFFRACTION98.81
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)
15.81693357694-1.098942621430.6373207834034.756730850471.151247110175.35940801664-0.00927215549530.2025178098770.57525216851-0.3843041356760.102546795933-0.201106083976-1.109009047010.706101232253-0.1199204192710.809347950718-0.1566595800070.09375567353750.4984531987910.04674747963550.48191221671711.251792942663.053376111939.3669656522
20.6980702842830.319162294095-0.05618289309311.200661340240.08875070682433.806980572740.07802137331480.09291558462530.0648067797808-0.269683964110.024647949679-0.0123610141632-0.3168695852460.108837941314-0.08306198062020.5402718374650.1324041552430.00447746084180.4667987797480.01712684157120.3909456979712.0310329035848.306177588441.374433532
32.271101784390.3687643980720.5646070212212.73486518755-0.0347872658883.838917407670.05032532893850.183740243803-0.253863199173-0.2062071813350.0576867924879-0.009064904247970.694266813108-0.129217911612-0.06117704119940.5893510738180.111472610738-0.04149441034770.435392429924-0.03534662629550.366281149224-3.6077637095827.017359422838.9829334157
44.03146408632-0.442386067761-0.09135482916291.36013317291.160063287451.73596244613-0.0498738618911-0.135906879278-0.313756844390.1828174159290.213486966368-0.01678223617980.504124133790.260155402748-0.1339462915780.4487348305170.233947037018-0.03323569270220.377466618658-0.0001741141925340.44151074449614.951334352418.779636989775.9414477577
56.282486391450.342626320158-2.057076022665.74540974547-0.4445743133861.03524692878-0.07348688460040.00530365856865-0.172609803833-0.162212191845-0.1118141910150.2982182521320.233307297545-0.1911285481850.1928876367820.3667149357820.187492657672-0.01601191825640.2388197104820.02135422538120.368738732475.88960677322.216124948674.2654492574
60.660278633261-0.2588909095870.2067340357121.302831827710.1281166978351.123719970230.00516359993454-0.02663490739570.04855095463280.02197498119020.009341357694430.01966949410350.0151475991860.000351157806677-0.01219094132430.3219997356460.1268743959870.0141962417140.4057599561780.007369876856410.378703524946-1.1670343711942.549060503974.4305896908
76.872840848913.39144712330.3408147107378.11027166321-0.8330991362420.4093982961560.0367219607111-0.1055767228050.460897760035-0.145656010096-0.05430140821450.349327718732-0.0968453995885-0.003865665443820.03174382810080.3632072343060.1958469408720.04297742205690.407671828885-0.04288290149430.274272949348-8.1089533078454.668891539171.2100821604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 324 )
4X-RAY DIFFRACTION4chain 'B' and (resid 17 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 91 )
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 291 )
7X-RAY DIFFRACTION7chain 'B' and (resid 292 through 324 )

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