[English] 日本語
Yorodumi
- PDB-7lpq: Crystal structure of Cryptococcus neoformans sterylglucosidase 1 ... -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more