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- PDB-5l7u: Crystal structure of BvGH123 with bound GalNAc -

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Basic information

Entry
Database: PDB / ID: 5l7u
TitleCrystal structure of BvGH123 with bound GalNAc
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / TIM barrel / BACON
Function / homologyGlycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / 2-acetamido-2-deoxy-beta-D-galactopyranose / Uncharacterized protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoth, C. / Petricevic, M. / John, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
CitationJournal: Chem. Commun. (Camb.) / Year: 2016
Title: Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation.
Authors: Roth, C. / Petricevic, M. / John, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: 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 10, 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: Glycoside hydrolase
B: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,1315
Polymers132,6532
Non-polymers4783
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-12 kcal/mol
Surface area43770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.345, 142.207, 145.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase /


Mass: 66326.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Gene: BVU_2198
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A6L2E5
#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.3 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M BisTRis pH 6.0-7.0 17 % PEG MME2k 10 mM GalNAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→65 Å / Num. obs: 68163 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l7r

5l7r


Resolution: 2.1→64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.183
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 3283 4.8 %RANDOM
Rwork0.1927 ---
obs0.1943 68085 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.13 Å2 / Biso mean: 52.2065 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å2-0 Å2-0 Å2
2--1.08 Å2-0 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9016 0 31 179 9226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029316
X-RAY DIFFRACTIONr_bond_other_d00.028724
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.94512637
X-RAY DIFFRACTIONr_angle_other_deg3.661320155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86651116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89724.354418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.537151622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6981540
X-RAY DIFFRACTIONr_chiral_restr0.0930.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110369
X-RAY DIFFRACTIONr_gen_planes_other0.0130.022145
X-RAY DIFFRACTIONr_mcbond_it1.3692.9344470
X-RAY DIFFRACTIONr_mcbond_other1.3692.9344469
X-RAY DIFFRACTIONr_mcangle_it2.184.3935584
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 240 -
Rwork0.322 4730 -
all-4970 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0278-0.7579-0.42542.86520.23262.37040.02750.0127-0.0720.05270.0306-0.0719-0.05920.0667-0.05820.1143-0.01040.030.01760.01170.0929-5.60319.334-22.718
20.5018-0.1170.01222.8221-1.84511.71790.0048-0.06710.01050.24150.043-0.0405-0.25130.0674-0.04790.1452-0.01080.01840.0252-0.0070.0801-13.198.6282.253
31.984-0.56420.22374.3067-0.83071.3950.08870.0676-0.07180.0240.18370.8263-0.3034-0.4055-0.27250.21430.0670.07310.18020.12110.254-26.775-3.68812.651
41.956-0.7982-0.50631.6671-0.33931.51930.06740.1842-0.03860.03740.07660.474-0.1787-0.3724-0.14410.17670.02860.03910.09740.04860.2084-26.94817.041-9.537
52.34210.28480.57922.8998-0.54111.82050.0873-0.0851-0.6174-0.0573-0.18260.22530.1326-0.18110.09530.2038-0.01080.01810.0465-0.02080.4658-13.076-58.53928.868
61.127-0.0760.01753.6483-1.70191.42360.0494-0.0074-0.07820.1162-0.2083-0.07730.02680.10220.15880.0758-0.0184-0.0040.05640.01420.0638-5.786-28.65126.142
75.41510.9483-3.63232.3455-1.77046.4040.06390.0891-0.22690.0888-0.3444-0.53540.09890.47790.28050.1473-0.0494-0.09440.16340.10570.22718.936-17.35324.774
81.44480.0175-0.01563.422-0.26970.96650.0662-0.059-0.25740.2671-0.2998-0.78040.09480.43330.23350.1715-0.0039-0.03060.21210.15470.3647.188-44.43132.508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 174
2X-RAY DIFFRACTION2A175 - 305
3X-RAY DIFFRACTION3A306 - 381
4X-RAY DIFFRACTION4A382 - 563
5X-RAY DIFFRACTION5B1 - 178
6X-RAY DIFFRACTION6B179 - 324
7X-RAY DIFFRACTION7B325 - 379
8X-RAY DIFFRACTION8B380 - 563

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