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- PDB-7lpq: Crystal structure of Cryptococcus neoformans sterylglucosidase 1 ... -

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Basic information

Entry
Database: PDB / ID: 7lpq
TitleCrystal structure of Cryptococcus neoformans sterylglucosidase 1 with hit 9
ComponentsCytoplasmic protein
KeywordsHYDROLASE / glucosidase / sterylglucosidase
Function / homology
Function and homology information


ergosteryl 3-beta-D-glucoside catabolic process / steryl-beta-glucosidase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-YAJ / Cytoplasmic protein
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPereira de Sa, N. / Del Poeta, M. / Airola, M.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 AI125770 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R35GM128666 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structure and inhibition of Cryptococcus neoformans sterylglucosidase to develop antifungal agents.
Authors: Pereira de Sa, N. / Taouil, A. / Kim, J. / Clement, T. / Hoffmann, R.M. / Burke, J.E. / Rizzo, R.C. / Ojima, I. / Del Poeta, M. / Airola, M.V.
History
DepositionFeb 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic protein
B: Cytoplasmic protein
C: Cytoplasmic protein
D: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,55414
Polymers356,7924
Non-polymers1,76210
Water31,9771775
1
A: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7265
Polymers89,1981
Non-polymers5284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7024
Polymers89,1981
Non-polymers5043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5172
Polymers89,1981
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6093
Polymers89,1981
Non-polymers4112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.417, 133.314, 130.303
Angle α, β, γ (deg.)90.000, 94.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytoplasmic protein


Mass: 89198.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05607 / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: J9W473
#2: Chemical
ChemComp-YAJ / ~{N}-[(3~{R},5~{S})-5-(hydroxymethyl)-1-methyl-pyrrolidin-3-yl]-2-(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)ethanamide


Mass: 319.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1775 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG8000, MgCl2, Tris 7.5, hit 9

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.32→43.3 Å / Num. obs: 144484 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.098 / Rrim(I) all: 0.181 / Χ2: 0.82 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible allCC1/2
2.32-2.363.40.9871.471340.6251.1710.799.7
12.71-43.33.30.03818.49000.0270.0470.6696.70.978

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LPO

7lpo


Resolution: 2.32→43.3 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 6957 5.06 %
Rwork0.1811 130579 -
obs0.1837 137536 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.81 Å2 / Biso mean: 38.3453 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 2.32→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23064 0 247 1775 25086
Biso mean--41.45 37.43 -
Num. residues----2906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.350.33311990.28474000419987
2.35-2.370.32912230.28684054427789
2.37-2.40.29132140.27624097431190
2.4-2.430.3192340.26474018425289
2.43-2.470.28342270.2474126435390
2.47-2.50.28972210.24784072429390
2.5-2.540.30762200.24664135435590
2.54-2.570.32962080.23414149435791
2.57-2.610.29532340.23054238447293
2.61-2.660.27922410.22414201444292
2.66-2.70.29522540.2144232448694
2.7-2.750.24622180.22034266448493
2.75-2.80.27232230.2034338456194
2.8-2.860.28812310.20934329456095
2.86-2.920.23472110.19424375458696
2.92-2.990.26092310.18574398462996
2.99-3.070.23742330.18074424465797
3.07-3.150.22112520.17564411466397
3.15-3.240.2272320.17084462469498
3.24-3.350.21132260.16644539476598
3.35-3.470.20882210.15694480470198
3.47-3.60.20252290.1524589481899
3.6-3.770.20572330.13744561479499
3.77-3.970.18352730.13984521479499
3.97-4.220.16642580.131345444802100
4.22-4.540.16532580.126245454803100
4.54-50.18752640.131345864850100
5-5.720.20392450.16845964841100
5.72-7.20.2452320.197446334865100
7.2-43.30.28622120.21174660487299
Refinement TLS params.Method: refined / Origin x: -0.9483 Å / Origin y: 9.7018 Å / Origin z: 30.7549 Å
111213212223313233
T0.2373 Å20.0043 Å20.0131 Å2-0.1975 Å20.0008 Å2--0.2365 Å2
L0.2446 °2-0.0033 °20.0524 °2-0.0163 °2-0.0057 °2--0.0196 °2
S-0.004 Å °0.0098 Å °0.0585 Å °-0.0018 Å °-0.0031 Å °-0.0003 Å °-0.0116 Å °-0.0168 Å °0.01 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 1101
2X-RAY DIFFRACTION1allB4 - 1101
3X-RAY DIFFRACTION1allC4 - 830
4X-RAY DIFFRACTION1allC901
5X-RAY DIFFRACTION1allD5 - 1001
6X-RAY DIFFRACTION1allS1 - 1891
7X-RAY DIFFRACTION1allE1

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