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

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Basic information

Entry
Database: PDB / ID: 7lpo
TitleCrystal structure of Cryptococcus neoformans sterylglucosidase 1 with tris
ComponentsCytoplasmic proteinCytoplasm
KeywordsHYDROLASE / glucosidase / sterylglucosidase
Function / homology
Function and homology information


carbohydrate derivative catabolic process / steryl-beta-glucosidase activity / lipid 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
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)357,3059
Polymers356,7924
Non-polymers5135
Water39,1112171
1
A: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3202
Polymers89,1981
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3443
Polymers89,1981
Non-polymers1462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3202
Polymers89,1981
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3202
Polymers89,1981
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.597, 126.606, 126.655
Angle α, β, γ (deg.)90.000, 95.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytoplasmic protein / Cytoplasm


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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2171 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12 % PEG8000, 0.2M MgCl2, 0.1 M Tris 7.5 / Temp details: RT

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.13→47.28 Å / Num. obs: 171606 / % possible obs: 99.4 % / Redundancy: 3.2 % / CC1/2: 0.969 / CC star: 0.992 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.091 / Rrim(I) all: 0.133 / Χ2: 0.93 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.13-2.172.30.5931.476940.6020.4630.7570.9490.5
11.67-47.283.30.0331510950.990.0220.0390.2998.4

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→47.28 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 8287 4.97 %
Rwork0.157 158430 -
obs0.159 166717 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.68 Å2 / Biso mean: 30.8908 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 2.13→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23076 0 81 2171 25328
Biso mean--33.92 35.66 -
Num. residues----2908
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 (%)
2.13-2.150.34422510.26994238448979
2.15-2.180.33022450.26314743498887
2.18-2.210.27782410.23064968520991
2.21-2.230.26962740.23235056533092
2.23-2.260.26792670.24315067533492
2.26-2.290.24812690.20655102537194
2.29-2.330.23612960.18875158545496
2.33-2.360.23792960.18525223551996
2.36-2.40.23122810.18255224550596
2.4-2.440.20822630.17475289555296
2.44-2.480.2312690.16785261553097
2.48-2.530.22772740.16995307558197
2.53-2.570.21372510.175306555797
2.57-2.630.22022660.1695359562598
2.63-2.680.20382370.16325392562998
2.68-2.750.19612860.15615350563698
2.75-2.810.19812460.15455422566899
2.81-2.890.17962790.15255404568399
2.89-2.980.19442550.15815392564799
2.98-3.070.22243020.15915398570099
3.07-3.180.19573070.15625421572899
3.18-3.310.19162610.147654665727100
3.31-3.460.17482920.138354295721100
3.46-3.640.16272980.126454995797100
3.64-3.870.16763200.122253935713100
3.87-4.170.15053170.119454515768100
4.17-4.590.142550.109655235778100
4.59-5.250.14682460.11955625808100
5.25-6.610.20533090.159454885797100
6.61-47.280.20993340.184955395873100
Refinement TLS params.Method: refined / Origin x: -12.5092 Å / Origin y: 46.5126 Å / Origin z: -32.6329 Å
111213212223313233
T0.1805 Å2-0.006 Å2-0.0044 Å2-0.1795 Å2-0.0016 Å2--0.1846 Å2
L0.0379 °20.0027 °2-0.0188 °2-0.0208 °2-0.0128 °2--0.035 °2
S-0.0038 Å °0.0158 Å °0.0094 Å °-0.0112 Å °0.0051 Å °0.0094 Å °-0.0033 Å °0.0094 Å °-0.0027 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 831
2X-RAY DIFFRACTION1allA901
3X-RAY DIFFRACTION1allB3 - 901
4X-RAY DIFFRACTION1allC1 - 834
5X-RAY DIFFRACTION1allC901
6X-RAY DIFFRACTION1allD3 - 830
7X-RAY DIFFRACTION1allD901
8X-RAY DIFFRACTION1allE1
9X-RAY DIFFRACTION1allS1 - 2419

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