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- PDB-5l7r: Crystal structure of BvGH123 -

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Basic information

Entry
Database: PDB / ID: 5l7r
TitleCrystal structure of BvGH123
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 / Uncharacterized protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsRoth, C. / Petricevic, M. / John, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K003836/1 United Kingdom
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 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: glycoside hydrolase
B: glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8395
Polymers132,6532
Non-polymers1863
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint6 kcal/mol
Surface area45780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.269, 147.794, 150.500
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 (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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Bis Tris pH6.5 17-19 % PEG MME 2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→75.25 Å / Num. obs: 106036 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Net I/σ(I): 9.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.93 / 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
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→67.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2120 2 %RANDOM
Rwork0.181 ---
obs0.18 105941 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.53 Å2 / Biso mean: 35.6513 Å2 / Biso min: 7.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→67.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9086 0 12 644 9742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.029341
X-RAY DIFFRACTIONr_bond_other_d00.028751
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.94112662
X-RAY DIFFRACTIONr_angle_other_deg3.638320215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6751124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24424.381420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.941151626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5041540
X-RAY DIFFRACTIONr_chiral_restr0.10.21358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110420
X-RAY DIFFRACTIONr_gen_planes_other0.0170.022152
X-RAY DIFFRACTIONr_mcbond_it1.0342.2984502
X-RAY DIFFRACTIONr_mcbond_other1.0332.2984501
X-RAY DIFFRACTIONr_mcangle_it1.5273.4415624
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 146 -
Rwork0.368 7585 -
all-7731 -
obs--99.96 %
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)
11.2391-0.8702-0.39413.06580.21692.65430.07070.0450.5468-0.20890.20920.2256-0.3221-0.0062-0.280.0551-0.0048-0.00070.04890.07170.3984-8.67366.60221.941
20.7120.0703-0.12081.6891-0.68220.46630.01750.06480.0933-0.25430.10670.22120.0738-0.1023-0.12420.04560.0027-0.0280.05820.02310.0429-5.17146.42324.021
31.0182-0.0440.13911.0453-1.30433.11140.0299-0.1095-0.0793-0.0512-0.0799-0.097-0.12060.16240.04990.0269-0.0080.01150.02310.01730.03296.55726.97942.335
40.94340.1370.00861.6497-0.58240.5454-0.0086-0.0291-0.0449-0.1622-0.0551-0.23490.09720.15540.06360.02560.02940.02060.07130.00090.035111.64838.97828.628
54.2850.00640.45814.76773.03895.76610.08580.5082-0.0746-0.46480.1787-0.4304-0.00110.6811-0.26440.17610.02150.10190.22370.05820.160316.15750.5477.955
61.0761-0.2749-0.15180.98040.01431.95210.02050.16720.0845-0.0595-0.059-0.1497-0.1860.36040.03850.0262-0.0136-0.00320.19180.00210.052225.74464.69253.506
70.658-0.08390.0860.736-0.45452.322-0.02620.01850.0041-0.0404-0.044-0.0714-0.23590.23590.07020.0367-0.025-0.00010.02650.01340.025720.80865.32679.724
87.6594-2.71022.56132.0231-1.65811.55860.12720.3065-0.3547-0.1655-0.00940.16140.17360.0288-0.11770.0323-0.00480.00810.06360.02860.07859.3749.3997.673
90.6802-0.1514-0.00460.35320.16961.9917-0.0083-0.0005-0.07390.0154-0.03210.1002-0.1367-0.17820.04040.0140.01010.00190.0171-0.00710.03356.87365.10776.186
103.6201-0.0861-0.28276.98771.04691.89830.02880.11880.38130.0192-0.05850.4269-0.4875-0.35210.02980.22530.0941-0.03290.20290.05570.09981.59578.94657.278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 53
2X-RAY DIFFRACTION2A54 - 283
3X-RAY DIFFRACTION3A284 - 337
4X-RAY DIFFRACTION4A338 - 511
5X-RAY DIFFRACTION5A512 - 563
6X-RAY DIFFRACTION6B2 - 172
7X-RAY DIFFRACTION7B173 - 305
8X-RAY DIFFRACTION8B306 - 336
9X-RAY DIFFRACTION9B337 - 516
10X-RAY DIFFRACTION10B517 - 563

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