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- PDB-7t66: Co-crystal structure of Chaetomium glucosidase with compound UV-4 -

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Basic information

Entry
Database: PDB / ID: 7t66
TitleCo-crystal structure of Chaetomium glucosidase with compound UV-4
ComponentsChaetomium alpha glucosidase
KeywordsHYDROLASE/INHIBITOR / alpha glucosidase I / Hydrolase / Inhibitor complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


mannosyl-oligosaccharide glucosidase / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation / endoplasmic reticulum membrane
Similarity search - Function
Glycosyl hydrolase family 63, C-terminal / Glycosyl hydrolase family 63, N-terminal / Glycosyl hydrolase family 63, N-terminal domain superfamily / Glycosyl hydrolase family 63 C-terminal domain / Glycosyl hydrolase family 63 N-terminal domain / Glycoside hydrolase family 63 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
N-9'-methoxynonyl-1-deoxynojirimycin / Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2022
Title: Identification of Endoplasmic Reticulum alpha-Glucosidase I from a Thermophilic Fungus as a Platform for Structure-Guided Antiviral Drug Design.
Authors: Karade, S.S. / Kolesnikov, A. / Treston, A.M. / Mariuzza, R.A.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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: Chaetomium alpha glucosidase
B: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,85418
Polymers186,6402
Non-polymers2,21416
Water10,575587
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A: Chaetomium alpha glucosidase
hetero molecules


  • defined by author
  • 94.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)94,3089
Polymers93,3201
Non-polymers9888
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaetomium alpha glucosidase
hetero molecules


  • defined by author
  • 94.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)94,5469
Polymers93,3201
Non-polymers1,2268
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.587, 178.395, 180.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1306-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Chaetomium alpha glucosidase


Mass: 93319.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061620 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: G0SFD1
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 602 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-6A9 / N-9'-methoxynonyl-1-deoxynojirimycin


Mass: 319.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H33NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 Bis Tris pH 6.5, 1.6-2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.19→46.78 Å / Num. obs: 111323 / % possible obs: 99.73 % / Redundancy: 6.8 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04429 / Rpim(I) all: 0.01836 / Rrim(I) all: 0.04802 / Net I/σ(I): 18.4
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.2406 / Num. unique obs: 10928 / CC1/2: 0.978 / CC star: 0.994 / Rpim(I) all: 0.0979 / Rrim(I) all: 0.2601 / % possible all: 98.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J5T

4j5t


Resolution: 2.19→46.78 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.849 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 5495 4.9 %RANDOM
Rwork0.1872 ---
obs0.1894 105826 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.83 Å2 / Biso mean: 34.141 Å2 / Biso min: 16.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0 Å2
2--1.63 Å20 Å2
3----2.01 Å2
Refinement stepCycle: final / Resolution: 2.19→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12138 0 134 587 12859
Biso mean--55.55 39.66 -
Num. residues----1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01212657
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.64117241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11951538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7622.299683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.435151931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961574
X-RAY DIFFRACTIONr_chiral_restr0.1110.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029927
LS refinement shellResolution: 2.192→2.249 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 376 -
Rwork0.229 7708 -
all-8084 -
obs--98.49 %

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