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- PDB-6k35: Crystal structure of GH20 exo beta-N-acetylglucosaminidase from V... -

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Basic information

Entry
Database: PDB / ID: 6k35
TitleCrystal structure of GH20 exo beta-N-acetylglucosaminidase from Vibrio harveyi in complex with NAG-thiazoline
ComponentsBeta-N-acetylglucosaminidase Nag2
KeywordsHYDROLASE / Anti-bacterial agent
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / lysosome / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NGT / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsMeekrathok, P. / Stubbs, K.A. / Bulmer, D.M. / van den Berg, B. / Suginta, W.
CitationJournal: Febs J. / Year: 2020
Title: NAG-thiazoline is a potent inhibitor of the Vibrio campbellii GH20 beta-N-Acetylglucosaminidase.
Authors: Meekrathok, P. / Stubbs, K.A. / Aunkham, A. / Kaewmaneewat, A. / Kardkuntod, A. / Bulmer, D.M. / van den Berg, B. / Suginta, W.
History
DepositionMay 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylglucosaminidase Nag2
B: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5264
Polymers149,0882
Non-polymers4392
Water8,053447
1
A: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7632
Polymers74,5441
Non-polymers2191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint5 kcal/mol
Surface area24650 Å2
MethodPISA
2
B: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7632
Polymers74,5441
Non-polymers2191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint5 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 145.040, 88.680
Angle α, β, γ (deg.)90.00, 109.66, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-N-acetylglucosaminidase Nag2


Mass: 74543.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D9ISE0, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium Fluoride, 0.1M Bis Tris Propane pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.36→29.35 Å / Num. obs: 60694 / % possible obs: 99.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 34.11 Å2 / Net I/σ(I): 6.09
Reflection shellResolution: 2.36→2.44 Å / Num. unique obs: 6032

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Processing

Software
NameVersionClassification
PHENIX1.8.2-1309refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCN

3rcn


Resolution: 2.36→29.35 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.37
RfactorNum. reflection% reflection
Rfree0.2649 2943 4.85 %
Rwork0.1937 --
obs0.1972 60668 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.36→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 0 28 447 10767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310596
X-RAY DIFFRACTIONf_angle_d1.41914411
X-RAY DIFFRACTIONf_dihedral_angle_d21.4553885
X-RAY DIFFRACTIONf_chiral_restr0.0641551
X-RAY DIFFRACTIONf_plane_restr0.0091874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.39870.39681040.29722806X-RAY DIFFRACTION100
2.3987-2.440.35761120.27982732X-RAY DIFFRACTION100
2.44-2.48440.34721460.26812771X-RAY DIFFRACTION100
2.4844-2.53210.3031480.24922716X-RAY DIFFRACTION100
2.5321-2.58380.27271410.2392769X-RAY DIFFRACTION100
2.5838-2.63990.31921380.23132701X-RAY DIFFRACTION100
2.6399-2.70130.29511250.23342786X-RAY DIFFRACTION100
2.7013-2.76880.32211530.23412728X-RAY DIFFRACTION100
2.7688-2.84360.29631700.23162716X-RAY DIFFRACTION100
2.8436-2.92720.28941460.22452706X-RAY DIFFRACTION100
2.9272-3.02160.3111360.21542733X-RAY DIFFRACTION100
3.0216-3.12950.29571720.20552745X-RAY DIFFRACTION100
3.1295-3.25460.28651550.19692706X-RAY DIFFRACTION100
3.2546-3.40250.26521480.1862756X-RAY DIFFRACTION100
3.4025-3.58160.25481190.17972762X-RAY DIFFRACTION100
3.5816-3.80560.25171320.16472755X-RAY DIFFRACTION100
3.8056-4.09870.25971640.16322731X-RAY DIFFRACTION100
4.0987-4.50990.21141320.14852780X-RAY DIFFRACTION100
4.5099-5.15940.18481490.142742X-RAY DIFFRACTION100
5.1594-6.48870.23971190.18722776X-RAY DIFFRACTION100
6.4887-29.35520.25071340.19632808X-RAY DIFFRACTION99

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