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- PDB-5l7v: Crystal Structure of BvGH123 with bond transition state analog Ga... -

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Basic information

Entry
Database: PDB / ID: 5l7v
TitleCrystal Structure of BvGH123 with bond transition state analog Galthiazoline.
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 / Chem-GNL / Uncharacterized protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: glycoside hydrolase
B: glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4034
Polymers128,9652
Non-polymers4392
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area45430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.504, 148.386, 147.659
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: 64482.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / NBRC 14291 / NCTC 11154) (bacteria)
Gene: BVU_2198
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A6L2E5
#2: Chemical ChemComp-GNL / (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0. 1 M BisTris 16-20 % PEG MME2k / PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→74.19 Å / Num. obs: 51335 / % possible obs: 93.4 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 6 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 1.1 / % possible all: 63.6

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Processing

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

5l7r


Resolution: 2.3→74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.224
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1098 2.1 %RANDOM
Rwork0.1873 ---
obs0.188 51273 92.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 171.54 Å2 / Biso mean: 80.9238 Å2 / Biso min: 25.87 Å2
Baniso -1Baniso -2Baniso -3
1--4.55 Å2-0 Å2-0 Å2
2--2.16 Å2-0 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9077 0 28 27 9132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.029353
X-RAY DIFFRACTIONr_bond_other_d00.028750
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.94512688
X-RAY DIFFRACTIONr_angle_other_deg3.666320218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85851123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80824.368419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.924151624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9921540
X-RAY DIFFRACTIONr_chiral_restr0.0940.21367
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110415
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022149
X-RAY DIFFRACTIONr_mcbond_it1.9654.4174498
X-RAY DIFFRACTIONr_mcbond_other1.9654.4174497
X-RAY DIFFRACTIONr_mcangle_it3.0746.6275619
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 26 -
Rwork0.369 2428 -
all-2454 -
obs--61.46 %
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)
12.582-1.161-0.47894.2502-0.60474.95030.0010.10561.0619-0.38340.13640.2442-0.63020.1295-0.13750.16680.0008-0.10650.18290.01380.7523-8.97666.85521.63
22.2186-0.9580.15133.0677-1.45431.78070.14140.16370.3403-0.5335-0.02830.19510.0857-0.1107-0.11310.1370.0364-0.05420.12040.05770.3879-5.84349.78920.834
32.07020.0031-0.34572.3921-1.77543.25830.1231-0.066-0.0394-0.316-0.2166-0.31020.270.50330.09340.13810.1015-0.00080.17870.03040.302611.97227.86234.95
43.623-0.1751-1.05662.8592-0.64273.74630.19070.23520.5343-0.6402-0.1698-0.4182-0.05680.6256-0.02080.21980.05180.03610.2010.0990.46729.08750.1818.239
51.3553-0.63170.28732.9901-0.28993.89040.10670.78720.0182-0.2244-0.1182-0.1393-0.31340.91950.01150.2283-0.00240.08280.9032-0.07660.477326.59165.56751.406
61.7888-0.49240.89211.4955-0.89973.53490.02340.0466-0.14930.0131-0.06820.0919-0.2881-0.04780.04480.08490.01210.04690.1158-0.02430.284611.59363.94683.708
72.1278-0.38331.1052.0414-0.39883.36930.0030.5155-0.1222-0.22750.0653-0.018-0.20010.412-0.06830.12110.02570.05220.3248-0.06710.260513.93964.14664.194
83.5621-1.5667-0.314610.79171.68234.3169-0.05170.1440.485-0.0487-0.1060.6452-0.8552-0.35210.15780.49660.0963-0.05310.55520.04230.4641.64679.5655.681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION2A53 - 261
3X-RAY DIFFRACTION3A262 - 432
4X-RAY DIFFRACTION4A433 - 563
5X-RAY DIFFRACTION5B2 - 182
6X-RAY DIFFRACTION6B183 - 432
7X-RAY DIFFRACTION7B433 - 515
8X-RAY DIFFRACTION8B516 - 563

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