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- PDB-6t7g: Bacteroides salyersiae GH164 beta-mannosidase in complex with man... -

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Basic information

Entry
Database: PDB / ID: 6t7g
TitleBacteroides salyersiae GH164 beta-mannosidase in complex with mannoimidazole
ComponentsGlyco_hydro_42M domain-containing protein
KeywordsHYDROLASE / Beta-mannosidase Glycoside Hydrolase
Function / homologyGlycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / beta-galactosidase activity / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily / carbohydrate metabolic process / Chem-MVL / Beta-galactosidase trimerisation domain-containing protein
Function and homology information
Biological speciesBacteroides salyersiae CL02T12C01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)462,46734
Polymers460,0606
Non-polymers2,40728
Water30,0131666
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)231,29618
Polymers230,0303
Non-polymers1,26615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-40 kcal/mol
Surface area68070 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)231,17116
Polymers230,0303
Non-polymers1,14113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-41 kcal/mol
Surface area67490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.710, 104.743, 170.568
Angle α, β, γ (deg.)92.290, 97.273, 106.301
Int Tables number1
Space group name H-MP1

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Components

#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 CL02T12C01 (bacteria)
Gene: HMPREF1071_03408 / Production host: Escherichia coli (E. coli) / References: UniProt: I9SUA3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MVL / (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / Mannoimidazole


Mass: 200.192 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1666 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium tartrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.8→168.66 Å / Num. obs: 424506 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 21158 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6t5o

6t5o


Resolution: 1.8→168.66 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2312 21073 4.964 %
Rwork0.2065 --
all0.208 --
obs-424505 99.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.475 Å2
Baniso -1Baniso -2Baniso -3
1-2.236 Å21.593 Å20.199 Å2
2--0.068 Å20.686 Å2
3----3.312 Å2
Refinement stepCycle: LAST / Resolution: 1.8→168.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31572 0 154 1666 33392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01332604
X-RAY DIFFRACTIONr_bond_other_d0.0350.01729402
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.63844113
X-RAY DIFFRACTIONr_angle_other_deg2.311.57268509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21953922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1723.9231629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.102155534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9751591
X-RAY DIFFRACTIONr_chiral_restr0.0710.24190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0236204
X-RAY DIFFRACTIONr_gen_planes_other0.0110.026976
X-RAY DIFFRACTIONr_nbd_refined0.20.25826
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.225833
X-RAY DIFFRACTIONr_nbtor_refined0.170.215696
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.212865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21526
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.213
X-RAY DIFFRACTIONr_nbd_other0.2730.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.28
X-RAY DIFFRACTIONr_mcbond_it3.3433.9915712
X-RAY DIFFRACTIONr_mcbond_other3.3423.9915711
X-RAY DIFFRACTIONr_mcangle_it4.3845.97919626
X-RAY DIFFRACTIONr_mcangle_other4.3845.97919627
X-RAY DIFFRACTIONr_scbond_it4.0054.38516892
X-RAY DIFFRACTIONr_scbond_other4.0054.38516893
X-RAY DIFFRACTIONr_scangle_it5.8216.40424487
X-RAY DIFFRACTIONr_scangle_other5.8216.40424488
X-RAY DIFFRACTIONr_lrange_it6.99945.69236389
X-RAY DIFFRACTIONr_lrange_other6.9945.54336101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.35415200.341298130.341313720.6340.64899.87570.343
1.847-1.8970.31315170.306291260.307306430.7430.7431000.306
1.897-1.9520.30514820.292282620.293297440.7760.7791000.288
1.952-2.0120.28214030.26275850.261289880.8210.8311000.255
2.012-2.0780.27314550.257265650.258280200.840.8491000.249
2.078-2.1510.26213340.233257390.234270730.8750.8831000.226
2.151-2.2320.27112850.238249300.24262150.8720.8871000.227
2.232-2.3240.4712360.466239360.466251720.830.8361000.41
2.324-2.4270.24511810.211229500.212241310.90.9121000.203
2.427-2.5450.23911030.2219590.202230620.9130.9231000.196
2.545-2.6830.24510870.208209170.21220040.9110.9221000.206
2.683-2.8460.24310650.192196210.194206860.9120.9291000.197
2.846-3.0420.21610010.191185270.192195280.930.9371000.201
3.042-3.2860.2229310.196172310.197181620.9280.9361000.209
3.286-3.5990.2168180.2158220.201166400.9370.9381000.218
3.599-4.0240.2047280.182144130.183151410.9380.9471000.204
4.024-4.6460.1816670.155126360.156133030.9510.9581000.182
4.646-5.6890.1735510.153106640.154112150.9580.9631000.182
5.689-8.0410.1754480.16282320.16386800.9590.9591000.198
8.041-168.6630.2132610.18145040.18347650.9350.9431000.209

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