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- PDB-6ezt: Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase D437A ... -

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Basic information

Entry
Database: PDB / ID: 6ezt
TitleCrystal structure of GH20 Exo beta-N-Acetylglucosaminidase D437A inactive mutant from Vibrio harveyi
ComponentsBeta-N-acetylglucosaminidase Nag2
KeywordsHYDROLASE / N-acetylglucosamine / inactive mutant
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
DI(HYDROXYETHYL)ETHER / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1106
Polymers148,5092
Non-polymers6014
Water7,638424
1
A: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5553
Polymers74,2551
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylglucosaminidase Nag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5553
Polymers74,2551
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.420, 129.240, 98.360
Angle α, β, γ (deg.)90.000, 112.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-N-acetylglucosaminidase Nag2


Mass: 74254.617 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): Escherichia coli type strain M15 (pREP4)
References: UniProt: D9ISE0, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 3.61 Å3/Da / Density % sol: 65.9 %
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: 2.6→91.09 Å / Num. obs: 63617 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.861 % / Biso Wilson estimate: 56.757 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.136 / Χ2: 0.926 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.677.1020.7752.1846750.8650.83599.7
2.67-2.747.0690.6032.7145700.9210.65199.8
2.74-2.826.9810.4733.2844500.9630.51199.7
2.82-2.916.8430.3933.9643320.9630.42599.8
2.91-36.5360.3244.7341960.9720.352100
3-3.116.7540.2665.8640240.9760.28899.7
3.11-3.226.8190.2217.0738900.9830.239100
3.22-3.367.0720.1738.9637660.9890.18799.9
3.36-3.517.060.14310.8236390.9910.15599.8
3.51-3.686.9480.12512.4134520.9920.13599.8
3.68-3.886.6680.11113.4232830.9910.12199.8
3.88-4.116.6020.10314.7331020.990.11399.8
4.11-4.396.8990.09716.2829400.9940.105100
4.39-4.757.0430.09417.5827220.9910.10199.5
4.75-5.26.8740.09217.7525220.9920.1100
5.2-5.816.4550.09116.8122790.9910.09999.5
5.81-6.716.6760.09417.1920010.990.10299.9
6.71-8.226.9990.08818.7117130.9920.09599.4
8.22-11.636.4890.0819.413260.990.08799.6
11.63-91.096.7960.07520.277350.9930.08198

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Processing

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

6ezr


Resolution: 2.6→91.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 23.637 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.406 / ESU R Free: 0.264
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 3180 5 %RANDOM
Rwork0.1949 ---
obs0.197 60437 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.18 Å2 / Biso mean: 64.279 Å2 / Biso min: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å2-0 Å22.04 Å2
2---6.58 Å20 Å2
3---2.15 Å2
Refinement stepCycle: final / Resolution: 2.6→91.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10280 0 40 426 10746
Biso mean--94.27 56.42 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910613
X-RAY DIFFRACTIONr_bond_other_d0.0020.029856
X-RAY DIFFRACTIONr_angle_refined_deg1.211.94714414
X-RAY DIFFRACTIONr_angle_other_deg0.907322718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22424.194527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.379151751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.851564
X-RAY DIFFRACTIONr_chiral_restr0.0650.21545
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022504
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 232 -
Rwork0.322 4431 -
all-4663 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 4.899 Å / Origin y: 13.1174 Å / Origin z: 27.4451 Å
111213212223313233
T0.017 Å20.0061 Å20.0135 Å2-0.0275 Å20.0145 Å2--0.0464 Å2
L0.1345 °20.0474 °20.0762 °2-0.2228 °20.1228 °2--0.2286 °2
S-0.0028 Å °-0.0087 Å °-0.0467 Å °-0.0099 Å °0.0628 Å °-0.0028 Å °-0.0425 Å °-0.0089 Å °-0.06 Å °

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