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- PDB-7mfl: Structure of the Clostridium perfringens GH89 in complex with bet... -

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Basic information

Entry
Database: PDB / ID: 7mfl
TitleStructure of the Clostridium perfringens GH89 in complex with beta-HNJNAc
ComponentsAlpha-N-acetylglucosaminidase family protein
KeywordsHYDROLASE/INHIBITOR / NAGLU / Clostridium perfringens / MPS IIIB / inhibitor / GH89 / glycoside hydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alpha-N-acetylglucosaminidase / Alpha-N-acetylglucosaminidase, N-terminal / Alpha-N-acetylglucosaminidase, C-terminal / Alpha-N-acetylglucosaminidase, tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain / Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain / NedA-like, galactose-binding domain / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. ...Alpha-N-acetylglucosaminidase / Alpha-N-acetylglucosaminidase, N-terminal / Alpha-N-acetylglucosaminidase, C-terminal / Alpha-N-acetylglucosaminidase, tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain / Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain / Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain / NedA-like, galactose-binding domain / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-Z8V / Alpha-N-acetylglucosaminidase family protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoraston, A.B.
CitationJournal: Chemistry / Year: 2021
Title: Iminosugar C-Glycosides Work as Pharmacological Chaperones of NAGLU, a Glycosidase Involved in MPS IIIB Rare Disease*.
Authors: Zhu, S. / Jagadeesh, Y. / Tran, A.T. / Imaeda, S. / Boraston, A. / Alonzi, D.S. / Poveda, A. / Zhang, Y. / Desire, J. / Charollais-Thoenig, J. / Demotz, S. / Kato, A. / Butters, T.D. / ...Authors: Zhu, S. / Jagadeesh, Y. / Tran, A.T. / Imaeda, S. / Boraston, A. / Alonzi, D.S. / Poveda, A. / Zhang, Y. / Desire, J. / Charollais-Thoenig, J. / Demotz, S. / Kato, A. / Butters, T.D. / Jimenez-Barbero, J. / Sollogoub, M. / Bleriot, Y.
History
DepositionApr 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Aug 11, 2021Group: Advisory / Database references / Category: database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Aug 18, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-N-acetylglucosaminidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,00811
Polymers103,0331
Non-polymers97510
Water15,367853
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-55 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 91.000, 252.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-N-acetylglucosaminidase family protein / CpGH89


Mass: 103033.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: CPF_0859 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2YU91

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Non-polymers , 5 types, 863 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-Z8V / N-[(2R,3S,4R,5R,6R)-4,5-dihydroxy-2,6-bis(hydroxymethyl)piperidin-3-yl]acetamide


Mass: 234.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.0 M ammonium sulfate, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 77514 / % possible obs: 97.4 % / Redundancy: 7 % / Biso Wilson estimate: 27.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.039 / Rrim(I) all: 0.023 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3675 / CC1/2: 0.728 / Rpim(I) all: 0.383 / Rrim(I) all: 0.643 / % possible all: 78

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MFK

7mfk


Resolution: 2→29.79 Å / SU ML: 0.2142 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2745 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1969 3832 4.95 %
Rwork0.1615 73613 -
obs0.1632 77445 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.21 Å2
Refinement stepCycle: LAST / Resolution: 2→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 55 853 8034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197356
X-RAY DIFFRACTIONf_angle_d0.51819968
X-RAY DIFFRACTIONf_chiral_restr0.04131023
X-RAY DIFFRACTIONf_plane_restr0.00241306
X-RAY DIFFRACTIONf_dihedral_angle_d3.89145978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.28391070.25692114X-RAY DIFFRACTION75.08
2.03-2.050.27721080.23332277X-RAY DIFFRACTION81.71
2.05-2.080.25981320.22042380X-RAY DIFFRACTION85.12
2.08-2.110.25861560.21942525X-RAY DIFFRACTION91.47
2.11-2.140.25351710.21042647X-RAY DIFFRACTION96.54
2.14-2.170.2111400.19792803X-RAY DIFFRACTION99.19
2.17-2.210.24251490.18792791X-RAY DIFFRACTION99.9
2.21-2.250.24741450.18312776X-RAY DIFFRACTION99.8
2.25-2.290.28091320.18122811X-RAY DIFFRACTION99.86
2.29-2.330.21581390.18342839X-RAY DIFFRACTION99.93
2.33-2.380.23331520.17612755X-RAY DIFFRACTION99.97
2.38-2.430.24171470.18392791X-RAY DIFFRACTION99.97
2.43-2.490.21461620.17492783X-RAY DIFFRACTION99.97
2.49-2.550.20721370.17852798X-RAY DIFFRACTION100
2.55-2.620.23841780.17132782X-RAY DIFFRACTION100
2.62-2.70.19341590.16872770X-RAY DIFFRACTION99.97
2.7-2.780.191060.17392837X-RAY DIFFRACTION100
2.78-2.880.22681630.16862789X-RAY DIFFRACTION100
2.88-30.21231590.17582779X-RAY DIFFRACTION100
3-3.140.23531450.16822845X-RAY DIFFRACTION100
3.14-3.30.18081210.16312778X-RAY DIFFRACTION100
3.3-3.510.17771100.14862873X-RAY DIFFRACTION100
3.51-3.780.16251460.13852787X-RAY DIFFRACTION100
3.78-4.160.14711300.12662833X-RAY DIFFRACTION100
4.16-4.760.13281320.1232818X-RAY DIFFRACTION100
4.76-5.980.16491430.14442811X-RAY DIFFRACTION100
5.98-29.790.18291630.15442821X-RAY DIFFRACTION99.93

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