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- PDB-7t6w: Crystal structure of Chaetomium Glucosidase I (apo) -

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Basic information

Entry
Database: PDB / ID: 7t6w
TitleCrystal structure of Chaetomium Glucosidase I (apo)
ComponentsChaetomium alpha glucosidase
KeywordsHYDROLASE / alpha glucosidase I / Chaetomium
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
Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaetomium alpha glucosidase
B: Chaetomium alpha glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,48118
Polymers186,6402
Non-polymers1,84216
Water30617
1
A: Chaetomium alpha glucosidase
hetero molecules


  • defined by author
  • 94.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)94,17210
Polymers93,3201
Non-polymers8539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaetomium alpha glucosidase
hetero molecules


  • defined by author
  • 94.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)94,3098
Polymers93,3201
Non-polymers9897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.152, 178.804, 180.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#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
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
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: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→47.06 Å / Num. obs: 68891 / % possible obs: 99.24 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.073 / Rrim(I) all: 0.18 / Net I/σ(I): 6.98
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 6443 / CC1/2: 0.58 / Rpim(I) all: 0.655 / % possible all: 93.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J5T

4j5t


Resolution: 2.6→47.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.414 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.429 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3515 5.1 %RANDOM
Rwork0.1895 ---
obs0.1926 65379 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.2 Å2 / Biso mean: 67.089 Å2 / Biso min: 30.87 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å20 Å2-0 Å2
2--0.14 Å20 Å2
3----5.36 Å2
Refinement stepCycle: final / Resolution: 2.6→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12019 0 109 17 12145
Biso mean--106.24 64.85 -
Num. residues----1532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212502
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.63717055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.79951537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02222.176671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.473151835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7851574
X-RAY DIFFRACTIONr_chiral_restr0.1110.21566
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029876
LS refinement shellResolution: 2.6→2.666 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.419 222 -
Rwork0.361 4347 -
obs--90.28 %

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