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- PDB-6t5o: Bacteroides salyersiae GH164 beta-mannosidase -

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Basic information

Entry
Database: PDB / ID: 6t5o
TitleBacteroides salyersiae GH164 beta-mannosidase
ComponentsGlyco_hydro_42M domain-containing protein
KeywordsHYDROLASE / Beta-mannosidase Glycoside Hydrolase
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Beta-galactosidase trimerisation domain-containing protein
Similarity search - Component
Biological speciesBacteroides salyersiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsArmstrong, Z. / Davies, G.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure and function ofBs164 beta-mannosidase fromBacteroides salyersiaethe founding member of glycoside hydrolase family GH164.
Authors: Armstrong, Z. / Davies, G.J.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Glyco_hydro_42M domain-containing protein
DDD: Glyco_hydro_42M domain-containing protein
CCC: Glyco_hydro_42M domain-containing protein
BBB: Glyco_hydro_42M domain-containing protein
FFF: Glyco_hydro_42M domain-containing protein
EEE: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,98145
Polymers460,0606
Non-polymers2,92139
Water34,2101899
1
AAA: Glyco_hydro_42M domain-containing protein
CCC: Glyco_hydro_42M domain-containing protein
BBB: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,58823
Polymers230,0303
Non-polymers1,55820
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12510 Å2
ΔGint-25 kcal/mol
Surface area66400 Å2
MethodPISA
2
DDD: Glyco_hydro_42M domain-containing protein
FFF: Glyco_hydro_42M domain-containing protein
EEE: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,39422
Polymers230,0303
Non-polymers1,36419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-24 kcal/mol
Surface area66290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.151, 103.912, 169.156
Angle α, β, γ (deg.)92.476, 97.336, 106.426
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules AAADDDCCCBBBFFFEEE

#1: Protein
Glyco_hydro_42M domain-containing protein


Mass: 76676.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides salyersiae (bacteria) / Gene: HMPREF1071_03408 / Production host: Escherichia coli (E. coli) / References: UniProt: I9SUA3

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Non-polymers , 7 types, 1938 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1899 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium tartrate pH 7.0, PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→66.847 Å / Num. obs: 332768 / % possible obs: 95.9 % / Redundancy: 3.2 % / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 1.91→1.94 Å / Num. unique obs: 16038 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
DIALSdata scaling
CRANK2phasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→66.847 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.177 / Average fsc free: 0.8836 / Average fsc work: 0.8937 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2207 16536 4.972 %
Rwork0.1903 316034 -
all0.192 --
obs-332570 95.965 %
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: 31.058 Å2
Baniso -1Baniso -2Baniso -3
1-2.902 Å21.631 Å2-0.568 Å2
2--0.566 Å2-0.758 Å2
3----3.93 Å2
Refinement stepCycle: LAST / Resolution: 1.91→66.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31500 0 181 1902 33583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01332517
X-RAY DIFFRACTIONr_bond_other_d0.0350.01729340
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.63843960
X-RAY DIFFRACTIONr_angle_other_deg2.3051.57268357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35753911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34823.9251623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.857155523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6141590
X-RAY DIFFRACTIONr_chiral_restr0.070.24167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0236109
X-RAY DIFFRACTIONr_gen_planes_other0.010.026949
X-RAY DIFFRACTIONr_nbd_refined0.2010.26457
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.227599
X-RAY DIFFRACTIONr_nbtor_refined0.1740.215756
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.213277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21980
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.218
X-RAY DIFFRACTIONr_nbd_other0.2560.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.217
X-RAY DIFFRACTIONr_mcbond_it2.4523.14815662
X-RAY DIFFRACTIONr_mcbond_other2.4523.14815661
X-RAY DIFFRACTIONr_mcangle_it3.4114.71619567
X-RAY DIFFRACTIONr_mcangle_other3.4124.71619568
X-RAY DIFFRACTIONr_scbond_it3.0213.4416855
X-RAY DIFFRACTIONr_scbond_other3.0213.4416854
X-RAY DIFFRACTIONr_scangle_it4.5345.02824393
X-RAY DIFFRACTIONr_scangle_other4.5345.02824393
X-RAY DIFFRACTIONr_lrange_it5.6236.40937440
X-RAY DIFFRACTIONr_lrange_other5.59936.27137046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.31612240.29723121X-RAY DIFFRACTION94.8051
1.96-2.0130.29311750.2822502X-RAY DIFFRACTION95.0082
2.013-2.0720.28511670.25921945X-RAY DIFFRACTION94.9587
2.072-2.1350.26811310.24221561X-RAY DIFFRACTION96.1362
2.135-2.2050.25410860.22420895X-RAY DIFFRACTION96.0624
2.205-2.2830.24910700.21720084X-RAY DIFFRACTION95.7671
2.283-2.3690.23910020.20219443X-RAY DIFFRACTION95.6984
2.369-2.4660.2359440.19219020X-RAY DIFFRACTION96.8844
2.466-2.5750.2359720.18918089X-RAY DIFFRACTION97.0668
2.575-2.7010.2269340.18517239X-RAY DIFFRACTION96.6238
2.701-2.8470.2318410.18316306X-RAY DIFFRACTION95.7719
2.847-3.020.2217950.1815736X-RAY DIFFRACTION97.4361
3.02-3.2280.2158140.18314634X-RAY DIFFRACTION97.2306
3.228-3.4870.2177210.1913536X-RAY DIFFRACTION96.2725
3.487-3.8190.2096740.18112597X-RAY DIFFRACTION97.3732
3.819-4.270.1885880.15711310X-RAY DIFFRACTION96.8577
4.27-4.930.1585070.1379933X-RAY DIFFRACTION95.6044
4.93-6.0360.1924110.1618314X-RAY DIFFRACTION95.4909
6.036-8.5310.1763240.1536339X-RAY DIFFRACTION93.9642
8.531-66.8470.1671560.1853430X-RAY DIFFRACTION92.2562

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