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

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Basic information

Entry
Database: PDB / ID: 6ezr
TitleCrystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi
ComponentsBeta-N-acetylglucosaminidase Nag2
KeywordsHYDROLASE / N-acetylglucosamine
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / 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
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 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 1.1Jan 17, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)149,0882
Polymers149,0882
Non-polymers00
Water16,628923
1
A: Beta-N-acetylglucosaminidase Nag2


Theoretical massNumber of molelcules
Total (without water)74,5441
Polymers74,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylglucosaminidase Nag2


Theoretical massNumber of molelcules
Total (without water)74,5441
Polymers74,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.150, 130.710, 98.480
Angle α, β, γ (deg.)90.000, 112.990, 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): M15 (pREP4) / References: UniProt: D9ISE0, beta-N-acetylhexosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 3.58 Å3/Da / Density % sol: 65.67 %
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: 0.9998 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: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.37→90.66 Å / Num. obs: 84783 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.811 % / Biso Wilson estimate: 44.968 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.159 / Χ2: 1.023 / Net I/σ(I): 9.93 / Num. measured all: 577490 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.37-2.437.0511.0872.2143641624361890.8411.17399.1
2.43-2.56.9870.9382.6442534613060880.8521.01499.3
2.5-2.576.9080.7773.1940739596258970.8940.84198.9
2.57-2.656.7140.6533.8738613579157510.8880.70899.3
2.65-2.746.5250.5394.5136542564556000.9110.58699.2
2.74-2.836.7280.4485.4336201540953810.940.48699.5
2.83-2.947.170.356.8337220522351910.9640.37899.4
2.94-3.067.0830.2658.1935442503250040.9760.28699.4
3.06-3.26.9890.1979.8733772485948320.9840.21399.4
3.2-3.356.8790.14712.1931864465346320.9880.1699.5
3.35-3.536.4140.11513.8827989437843640.9910.12599.7
3.53-3.756.6090.09815.6827533417841660.9930.10799.7
3.75-4.017.0680.08917.5727600391639050.9940.09799.7
4.01-4.336.9320.08218.7425338366336550.9950.08999.8
4.33-4.746.7070.0819.422664338633790.9930.08799.8
4.74-5.36.2310.08318.6718906304530340.9930.0999.6
5.3-6.126.6490.08318.5917793268426760.9930.09199.7
6.12-7.496.8220.07519.3915630229722910.9940.08199.7
7.49-10.66.2090.06420.0310947177117630.9960.0799.5
10.6-90.666.6210.05821.25652210079850.9970.06397.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rcn

3rcn


Resolution: 2.37→90.66 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.933 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 4215 5 %RANDOM
Rwork0.2143 ---
obs0.2166 80567 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 112.5 Å2 / Biso mean: 50.287 Å2 / Biso min: 23.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å21.34 Å2
2---3.19 Å2-0 Å2
3---1.25 Å2
Refinement stepCycle: final / Resolution: 2.37→90.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10286 0 0 923 11209
Biso mean---49.62 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910669
X-RAY DIFFRACTIONr_bond_other_d0.0060.029886
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.94414522
X-RAY DIFFRACTIONr_angle_other_deg0.912322792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92224.167540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.579151774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0851568
X-RAY DIFFRACTIONr_chiral_restr0.0710.21556
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022542
LS refinement shellResolution: 2.37→2.432 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 314 -
Rwork0.423 5869 -
all-6183 -
obs--99.1 %

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