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- PDB-6ry1: Crystal structure of Dfg5 from Chaetomium thermophilum in complex... -

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Basic information

Entry
Database: PDB / ID: 6ry1
TitleCrystal structure of Dfg5 from Chaetomium thermophilum in complex with mannose
ComponentsMannan endo-1,6-alpha-mannosidase
KeywordsHYDROLASE / Transglycosidase / Fungal Cell Wall / Plasma Membrane / GPI-anchor
Function / homology
Function and homology information


mannan endo-1,6-alpha-mannosidase / mannan endo-1,6-alpha-mannosidase activity / carbohydrate catabolic process / membrane
Similarity search - Function
Mannan endo-1,6-alpha-mannosidase / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
ACETATE ION / alpha-D-mannopyranose / TRIETHYLENE GLYCOL / Mannan endo-1,6-alpha-mannosidase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEssen, L.-O. / Vogt, M.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB987 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls.
Authors: Vogt, M.S. / Schmitz, G.F. / Varon Silva, D. / Mosch, H.U. / Essen, L.O.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.2Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mannan endo-1,6-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0166
Polymers49,5461
Non-polymers4705
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-11 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.855, 55.022, 80.458
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

ACT

21A-1323-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Mannan endo-1,6-alpha-mannosidase /


Mass: 49546.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0020800 / Production host: Escherichia coli B (bacteria) / Strain (production host): SHuffle T7 Express Competent
References: UniProt: G0S3F2, mannan endo-1,6-alpha-mannosidase
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 669 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammoniumiodide, PEG3350, Calcium acetate, MES, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2018 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.3→41.93 Å / Num. obs: 89845 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 10.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.038 / Net I/σ(I): 15.1
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.25 / Num. unique obs: 8959 / CC1/2: 0.928 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→41.926 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.6
RfactorNum. reflection% reflection
Rfree0.1252 4566 5.08 %
Rwork0.0958 --
obs0.0973 89815 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→41.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 28 665 3928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013477
X-RAY DIFFRACTIONf_angle_d1.1844748
X-RAY DIFFRACTIONf_dihedral_angle_d13.9671264
X-RAY DIFFRACTIONf_chiral_restr0.091481
X-RAY DIFFRACTIONf_plane_restr0.009623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.16061470.1162887X-RAY DIFFRACTION100
1.3148-1.33030.16871660.11122776X-RAY DIFFRACTION100
1.3303-1.34650.13031430.112840X-RAY DIFFRACTION100
1.3465-1.36350.14871690.10762807X-RAY DIFFRACTION100
1.3635-1.38150.16411520.10662833X-RAY DIFFRACTION100
1.3815-1.40040.18331660.10352829X-RAY DIFFRACTION100
1.4004-1.42040.14441690.09842786X-RAY DIFFRACTION100
1.4204-1.44160.13191470.09342853X-RAY DIFFRACTION100
1.4416-1.46410.13631430.08942852X-RAY DIFFRACTION100
1.4641-1.48810.14441460.08822828X-RAY DIFFRACTION100
1.4881-1.51380.1281690.08342823X-RAY DIFFRACTION100
1.5138-1.54130.11341430.07772826X-RAY DIFFRACTION100
1.5413-1.5710.11471610.07652886X-RAY DIFFRACTION100
1.571-1.6030.10281610.07362788X-RAY DIFFRACTION100
1.603-1.63790.11931630.07412804X-RAY DIFFRACTION100
1.6379-1.6760.12251500.07432864X-RAY DIFFRACTION100
1.676-1.71790.11241660.07642842X-RAY DIFFRACTION100
1.7179-1.76440.13441220.07882808X-RAY DIFFRACTION100
1.7644-1.81630.13181160.08382916X-RAY DIFFRACTION100
1.8163-1.87490.12421470.08222832X-RAY DIFFRACTION100
1.8749-1.94190.11021300.08042875X-RAY DIFFRACTION100
1.9419-2.01970.10631610.08252826X-RAY DIFFRACTION100
2.0197-2.11160.11221490.08562861X-RAY DIFFRACTION100
2.1116-2.22290.11981360.08442832X-RAY DIFFRACTION99
2.2229-2.36220.11741590.0872836X-RAY DIFFRACTION99
2.3622-2.54450.11581580.09422829X-RAY DIFFRACTION99
2.5445-2.80050.12261580.10042880X-RAY DIFFRACTION99
2.8005-3.20570.131510.10522832X-RAY DIFFRACTION99
3.2057-4.03830.10861640.10282859X-RAY DIFFRACTION99
4.0383-41.9480.14851540.13462939X-RAY DIFFRACTION99

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