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- PDB-6hpd: The structure of a beta-glucuronidase from glycoside hydrolase fa... -

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Basic information

Entry
Database: PDB / ID: 6hpd
TitleThe structure of a beta-glucuronidase from glycoside hydrolase family 2
ComponentsBeta-galactosidase (GH2)
KeywordsHYDROLASE / GH2 / glycoside hydrolase / glucuronidase
Function / homology
Function and homology information


beta-glucuronidase / beta-glucuronidase activity / carbohydrate metabolic process / periplasmic space / metal ion binding
Similarity search - Function
Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich ...Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
BROMIDE ION / Beta-glucuronidase
Similarity search - Component
Biological speciesFormosa agariphila KMM 3901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsRobb, C.S. / Gerlach, N. / Reisky, L. / Bornshoeru, U. / Hehemann, J.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationHE 7217/1-1 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan.
Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, ...Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, M.D. / Trautwein-Schult, A. / Becher, D. / Schweder, T. / Bornscheuer, U.T. / Hehemann, J.H.
History
DepositionSep 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Beta-galactosidase (GH2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9603
Polymers112,8551
Non-polymers1042
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-10 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.929, 67.170, 96.720
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-galactosidase (GH2)


Mass: 112855.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Formosa agariphila KMM 3901 (bacteria) / Gene: BN863_22060 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2KN75, beta-galactosidase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium Bromide, 0.1M BIS-TRIS pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.43→96.2 Å / Num. obs: 37999 / % possible obs: 99.5 % / Redundancy: 10 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.3
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 3961 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dmy

5dmy


Resolution: 2.43→96.2 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.597 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21149 1961 5.2 %RANDOM
Rwork0.16464 ---
obs0.16704 36036 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.334 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å2-0 Å21.3 Å2
2---1.21 Å20 Å2
3----1.59 Å2
Refinement stepCycle: 1 / Resolution: 2.43→96.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7575 0 2 489 8066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197787
X-RAY DIFFRACTIONr_bond_other_d00.027048
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.92410596
X-RAY DIFFRACTIONr_angle_other_deg3.632316206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4424.39385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7411538
X-RAY DIFFRACTIONr_chiral_restr0.0440.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218971
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021881
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_it1.2882.5873818
X-RAY DIFFRACTIONr_mcbond_other1.2882.5863817
X-RAY DIFFRACTIONr_mcangle_it2.1723.8744769
X-RAY DIFFRACTIONr_mcangle_other2.1713.8754770
X-RAY DIFFRACTIONr_scbond_it1.4542.5923969
X-RAY DIFFRACTIONr_scbond_other1.4542.5923969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3213.8565826
X-RAY DIFFRACTIONr_long_range_B_refined3.96320.2969190
X-RAY DIFFRACTIONr_long_range_B_other3.75820.189005
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.432→2.495 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 134 -
Rwork0.199 2654 -
obs--99.18 %

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