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- PDB-8bal: Niako3494, a bacterial protein structure in glycoside hydrolase f... -

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Basic information

Entry
Database: PDB / ID: 8bal
TitleNiako3494, a bacterial protein structure in glycoside hydrolase family 20
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / GH20 apo protein
Function / homologyGlycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glycoside hydrolase, family 20, catalytic core
Function and homology information
Biological speciesNiastella koreensis GR20-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDong, M.D. / Roth, C.R. / Jin, Y.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust218568/Z/19/Z United Kingdom
Royal SocietyRG170406 United Kingdom
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: Acs Catalysis / Year: 2022
Title: Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases
Authors: Zhang, Z. / Dong, M. / Zallot, R. / Blackburn, G.M. / Wang, N. / Wang, C. / Chen, L. / Baumann, P. / Wu, Z. / Wang, Z. / Fan, H. / Roth, C. / Jin, Y. / He, Y.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
D: Beta-N-acetylhexosaminidase
E: Beta-N-acetylhexosaminidase
F: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,04410
Polymers217,7165
Non-polymers3275
Water50428
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.987, 254.589, 139.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 43543.293 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Niastella koreensis GR20-10 (bacteria) / Strain: DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10 / Gene: Niako_3494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8TKW6, beta-N-acetylhexosaminidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein stock at 18mg/mL, in the precipitant: 0.1 M MMT buffer (DL-Malic acid, MES monohydrate, Tris base [ratio 1:2:2]), pH 6.0, 25 % w/v PEG 1500, protein to precipitant ratio 1:1, 1 uL ...Details: Protein stock at 18mg/mL, in the precipitant: 0.1 M MMT buffer (DL-Malic acid, MES monohydrate, Tris base [ratio 1:2:2]), pH 6.0, 25 % w/v PEG 1500, protein to precipitant ratio 1:1, 1 uL drop size, +50 nL 1:10000 diluted seed stock. Cryoprotectant used was made up with 20% PEG400 in 80% mother liquor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.3317
pseudo-merohedral221/2H+1/2K, 3/2H-1/2K, -L20.334
pseudo-merohedral331/2H-1/2K, -3/2H-1/2K, -L30.3342
ReflectionResolution: 2.27→73.49 Å / Num. obs: 120442 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.958 / Net I/σ(I): 6.3
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5852 / CC1/2: 0.336 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 2.27→73.49 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.811 / SU B: 5.491 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3561 6125 5.087 %
Rwork0.2828 114286 -
all0.287 --
obs-120411 99.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.39 Å2
Baniso -1Baniso -2Baniso -3
1-6.14 Å20 Å20 Å2
2--7.703 Å20 Å2
3----13.844 Å2
Refinement stepCycle: LAST / Resolution: 2.27→73.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13710 0 5 28 13743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01214097
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612978
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6519107
X-RAY DIFFRACTIONr_angle_other_deg0.5151.56730354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.3945.0031696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.329579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.057102462
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.82910640
X-RAY DIFFRACTIONr_chiral_restr0.0710.22032
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022799
X-RAY DIFFRACTIONr_nbd_refined0.2880.24410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2340.215711
X-RAY DIFFRACTIONr_nbtor_refined0.1980.26748
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.27799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2632
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.246
X-RAY DIFFRACTIONr_metal_ion_refined0.3420.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.257
X-RAY DIFFRACTIONr_nbd_other0.2010.2241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3470.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2030.21
X-RAY DIFFRACTIONr_mcbond_it2.8023.2846801
X-RAY DIFFRACTIONr_mcbond_other2.8023.2846801
X-RAY DIFFRACTIONr_mcangle_it4.124.928489
X-RAY DIFFRACTIONr_mcangle_other4.124.9218490
X-RAY DIFFRACTIONr_scbond_it2.1763.2177296
X-RAY DIFFRACTIONr_scbond_other2.1763.2177295
X-RAY DIFFRACTIONr_scangle_it3.2024.8410618
X-RAY DIFFRACTIONr_scangle_other3.2024.8410619
X-RAY DIFFRACTIONr_lrange_it5.83642.85917551
X-RAY DIFFRACTIONr_lrange_other5.83642.8617552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.3290.694120.6178389X-RAY DIFFRACTION99.2893
2.329-2.3930.6484720.5268110X-RAY DIFFRACTION100
2.393-2.4620.5144570.4667897X-RAY DIFFRACTION100
2.462-2.5380.5683910.3837821X-RAY DIFFRACTION100
2.538-2.6210.5223540.3547513X-RAY DIFFRACTION100
2.621-2.7130.4114040.2797226X-RAY DIFFRACTION100
2.713-2.8150.4633460.2957059X-RAY DIFFRACTION100
2.815-2.930.4093270.2526774X-RAY DIFFRACTION100
2.93-3.0610.3133400.236475X-RAY DIFFRACTION100
3.061-3.210.3522770.2616240X-RAY DIFFRACTION100
3.21-3.3830.2813450.2235890X-RAY DIFFRACTION100
3.383-3.5890.322810.2645615X-RAY DIFFRACTION100
3.589-3.8360.2882850.2395233X-RAY DIFFRACTION100
3.836-4.1430.3013120.2354877X-RAY DIFFRACTION100
4.143-4.5380.2782320.2254549X-RAY DIFFRACTION100
4.538-5.0730.2612370.2524110X-RAY DIFFRACTION100
5.073-5.8570.3392090.2533597X-RAY DIFFRACTION100
5.857-7.170.3162130.2413073X-RAY DIFFRACTION100
7.17-100.291450.2482439X-RAY DIFFRACTION100
8-73.490.307860.2981399X-RAY DIFFRACTION99.2647

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