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- PDB-6ezs: Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from V... -

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Basic information

Entry
Database: PDB / ID: 6ezs
TitleCrystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi in complex with N-acetylglucosamine
ComponentsBeta-N-acetylglucosaminidase Nag2
KeywordsHYDROLASE / N-acetylglucosamine / complex
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
MALONATE ION / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPorfetye, A.T. / Meekrathok, P. / Burger, M. / Vetter, I.R. / Suginta, W.
Funding support Thailand, Germany, 3items
OrganizationGrant numberCountry
Thailand Research FundPHD00842550 Thailand
DAADBRG578001 Germany
Thailand Research FundA/10/98020 Thailand
CitationJournal: To Be Published
Title: Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi
Authors: Meekrathok, P. / Porfetye, A.T. / Burger, M. / Vetter, I.R. / Suginta, W.
History
DepositionNov 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)149,7346
Polymers149,0882
Non-polymers6474
Water15,943885
1
A: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8673
Polymers74,5441
Non-polymers3232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8673
Polymers74,5441
Non-polymers3232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.250, 129.630, 100.000
Angle α, β, γ (deg.)90.000, 114.360, 90.000
Int Tables number4
Space group name H-MP1211

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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) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): strain M15 (pREP4) / References: UniProt: D9ISE0, beta-N-acetylhexosaminidase
#2: 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.: 2
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
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.5 / Details: 0.1 M sodium acetate pH 4.6, 1.4 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97889 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.5→48.02 Å / Num. obs: 72950 / % possible obs: 99.4 % / Redundancy: 4.7 % / CC1/2: 0.99 / Rsym value: 0.12 / Net I/σ(I): 9.71
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.53 % / Mean I/σ(I) obs: 3.17 / Num. unique obs: 5403 / CC1/2: 0.85 / Rsym value: 0.53 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
PHASERphasing
Cootmodel building
PDB_EXTRACT3.22data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ezr

6ezr


Resolution: 2.5→48.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / SU B: 19 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3648 5 %RANDOM
Rwork0.2001 ---
obs0.2024 69303 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.99 Å2 / Biso mean: 35.901 Å2 / Biso min: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.03 Å2
2---1.19 Å2-0 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 2.5→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10286 0 44 885 11215
Biso mean--30.88 34.99 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910647
X-RAY DIFFRACTIONr_bond_other_d0.0060.029856
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.94914479
X-RAY DIFFRACTIONr_angle_other_deg1.086322726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69251288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80924.237531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.017151762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2191564
X-RAY DIFFRACTIONr_chiral_restr0.0670.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022513
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 269 -
Rwork0.286 5119 -
all-5388 -
obs--99.72 %
Refinement TLS params.Method: refined / Origin x: 21.417 Å / Origin y: -13.1528 Å / Origin z: 17.8095 Å
111213212223313233
T0.004 Å20.002 Å20.0056 Å2-0.0104 Å2-0.001 Å2--0.0111 Å2
L0.0327 °2-0.0159 °20.0181 °2-0.1066 °2-0.0339 °2--0.0417 °2
S-0.0031 Å °0.0047 Å °-0.0107 Å °0.0045 Å °0.0192 Å °-0.0025 Å °-0.0106 Å °-0.0017 Å °-0.0161 Å °

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