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- PDB-5by3: A novel family GH115 4-O-Methyl-alpha-glucuronidase, BtGH115A, wi... -

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Basic information

Entry
Database: PDB / ID: 5by3
TitleA novel family GH115 4-O-Methyl-alpha-glucuronidase, BtGH115A, with specificity for decorated arabinogalactans
ComponentsBtGH115A
KeywordsSUGAR BINDING PROTEIN / Glycoside / hydrolase / arabinogalactans alpha-glucuronidase
Function / homology
Function and homology information


carbohydrate metabolic process / hydrolase activity
Similarity search - Function
Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 / Gylcosyl hydrolase 115 C-terminal domain / Glycosyl hydrolase 115 superfamily / Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 C-terminal domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / TIM Barrel ...Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 / Gylcosyl hydrolase 115 C-terminal domain / Glycosyl hydrolase 115 superfamily / Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 C-terminal domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Gylcosyl hydrolase 115 C-terminal domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å
AuthorsLammerts van Bueren, A. / Davies, G.J. / Turkenburg, J.P.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structural and Functional Characterization of a Novel Family GH115 4-O-Methyl-alpha-Glucuronidase with Specificity for Decorated Arabinogalactans.
Authors: Aalbers, F. / Turkenburg, J.P. / Davies, G.J. / Dijkhuizen, L. / Lammerts van Bueren, A.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BtGH115A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0793
Polymers89,9241
Non-polymers1552
Water1,78399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-23 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.770, 102.300, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BtGH115A


Mass: 89923.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_2958 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A3J6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 20% PEG 3350 0.2M sodium sulfate 0.01M glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795, 0.9798, 0.9682
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.96821
ReflectionResolution: 2.44→40 Å / Num. obs: 32214 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Net I/σ(I): 17.6
Reflection shellResolution: 2.44→2.51 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementResolution: 2.44→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.658 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26583 1630 5.1 %RANDOM
Rwork0.1894 ---
obs0.19326 30528 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.628 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å2-0 Å2
2---3.17 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.44→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 6 99 6169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196224
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9588427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3945764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88724.276297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.244151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3591540
X-RAY DIFFRACTIONr_chiral_restr0.130.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214723
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2255.2743041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.2517.9013801
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8845.4063183
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.41743.1349404
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.444→2.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 110 -
Rwork0.286 2231 -
obs--99.87 %

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