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- PDB-7omi: Bs164 in complex with mannocyclophellitol epoxide -

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Basic information

Entry
Database: PDB / ID: 7omi
TitleBs164 in complex with mannocyclophellitol epoxide
ComponentsGlyco_hydro_42M domain-containing protein
KeywordsHYDROLASE / Inhibitor complex
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
L(+)-TARTARIC ACID / Chem-VKN / Beta-galactosidase trimerisation domain-containing protein
Similarity search - Component
Biological speciesBacteroides salyersiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsArmstrong, Z. / Mcgregor, N. / Davies, G.
CitationJournal: Org.Biomol.Chem. / Year: 2022
Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases.
Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J.
History
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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
BBB: Glyco_hydro_42M domain-containing protein
CCC: Glyco_hydro_42M domain-containing protein
DDD: Glyco_hydro_42M domain-containing protein
EEE: Glyco_hydro_42M domain-containing protein
FFF: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,03959
Polymers460,0606
Non-polymers4,97953
Water38,4622135
1
AAA: Glyco_hydro_42M domain-containing protein
CCC: Glyco_hydro_42M domain-containing protein
DDD: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,61331
Polymers230,0303
Non-polymers2,58328
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-10 kcal/mol
Surface area67520 Å2
MethodPISA
2
BBB: Glyco_hydro_42M domain-containing protein
EEE: Glyco_hydro_42M domain-containing protein
FFF: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,42628
Polymers230,0303
Non-polymers2,39625
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-16 kcal/mol
Surface area67210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.452, 104.426, 170.781
Angle α, β, γ (deg.)92.292, 97.351, 106.554
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 12 molecules AAABBBCCCDDDEEEFFF

#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
#5: Sugar
ChemComp-VKN / (1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol


Type: saccharideCarbohydrate / Mass: 194.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 2182 molecules

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


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 150.087 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2135 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Ammonium tartrate pH 6.5 , 14 % PEG 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976284 Å / Relative weight: 1
ReflectionResolution: 1.76→65.87 Å / Num. obs: 438305 / % possible obs: 97.2 % / Redundancy: 3.1 % / CC1/2: 0.994 / Net I/σ(I): 7.6
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 21409 / CC1/2: 0.302

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T7G

6t7g


Resolution: 1.76→65.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2609 22062 5.035 %
Rwork0.2314 416151 -
all0.233 --
obs-438213 97.15 %
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: 34.914 Å2
Baniso -1Baniso -2Baniso -3
1-1.461 Å21.673 Å2-0.551 Å2
2--0.165 Å20.088 Å2
3----2.376 Å2
Refinement stepCycle: LAST / Resolution: 1.76→65.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31540 0 314 2135 33989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01332708
X-RAY DIFFRACTIONr_bond_other_d0.0350.01729439
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.64344233
X-RAY DIFFRACTIONr_angle_other_deg2.3111.57368605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34753922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57323.9191628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.339155522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1881591
X-RAY DIFFRACTIONr_chiral_restr0.0710.24223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0236252
X-RAY DIFFRACTIONr_gen_planes_other0.010.026965
X-RAY DIFFRACTIONr_nbd_refined0.20.25996
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.226083
X-RAY DIFFRACTIONr_nbtor_refined0.170.215642
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.212714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21880
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2210.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.215
X-RAY DIFFRACTIONr_nbd_other0.2640.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_mcbond_it2.8253.56215703
X-RAY DIFFRACTIONr_mcbond_other2.8253.56215702
X-RAY DIFFRACTIONr_mcangle_it3.7765.33519620
X-RAY DIFFRACTIONr_mcangle_other3.7775.33519621
X-RAY DIFFRACTIONr_scbond_it3.4333.85817005
X-RAY DIFFRACTIONr_scbond_other3.4333.85817006
X-RAY DIFFRACTIONr_scangle_it4.9855.65224613
X-RAY DIFFRACTIONr_scangle_other4.9855.65224614
X-RAY DIFFRACTIONr_lrange_it6.0640.97936911
X-RAY DIFFRACTIONr_lrange_other6.05740.94736863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8060.37217190.35930319X-RAY DIFFRACTION95.8619
1.806-1.8550.34115800.34129693X-RAY DIFFRACTION96.1211
1.855-1.9090.31914450.30228688X-RAY DIFFRACTION95.4361
1.909-1.9680.31714730.2928203X-RAY DIFFRACTION96.5324
1.968-2.0320.29514180.27827372X-RAY DIFFRACTION96.5719
2.032-2.1030.28414160.25726460X-RAY DIFFRACTION96.7782
2.103-2.1830.27913700.24725600X-RAY DIFFRACTION97.3014
2.183-2.2720.26313520.23624716X-RAY DIFFRACTION97.5124
2.272-2.3730.26512200.23123629X-RAY DIFFRACTION96.8394
2.373-2.4890.27112070.2322482X-RAY DIFFRACTION96.6031
2.489-2.6230.27611690.23821669X-RAY DIFFRACTION98.0256
2.623-2.7820.27111220.22220431X-RAY DIFFRACTION97.7638
2.782-2.9750.24210630.21419335X-RAY DIFFRACTION98.5792
2.975-3.2130.259010.22218031X-RAY DIFFRACTION98.4094
3.213-3.5190.2788840.2416640X-RAY DIFFRACTION98.6156
3.519-3.9340.2567780.23815036X-RAY DIFFRACTION98.7326
3.934-4.5430.2827020.2513177X-RAY DIFFRACTION98.0294
4.543-5.5630.1775380.15311253X-RAY DIFFRACTION98.8929
5.563-7.8630.1974560.1678702X-RAY DIFFRACTION98.9626
7.863-65.870.1982490.1684717X-RAY DIFFRACTION98.4731

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