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- PDB-3wux: Crystal structure of unsaturated glucuronyl hydrolase mutant D115... -

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Basic information

Entry
Database: PDB / ID: 3wux
TitleCrystal structure of unsaturated glucuronyl hydrolase mutant D115N/K370S from Streptococcus agalactiae
ComponentsUnsaturated chondroitin disaccharide hydrolase
KeywordsHYDROLASE / alpha6/alpha6-barrel
Function / homology
Function and homology information


unsaturated chondroitin disaccharide hydrolase / unsaturated chondroitin disaccharide hydrolase activity / chondroitin hydrolase activity / polysaccharide catabolic process
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Unsaturated chondroitin disaccharide hydrolase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsNakamichi, Y. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
CitationJournal: to be published
Title: Crystal structure of unsaturated glucuronyl hydrolase mutant D115N/K370S from Streptococcus agalactiae
Authors: Nakamichi, Y. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionMay 8, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unsaturated chondroitin disaccharide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,34313
Polymers46,5991
Non-polymers74512
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Unsaturated chondroitin disaccharide hydrolase
hetero molecules

A: Unsaturated chondroitin disaccharide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,68726
Polymers93,1972
Non-polymers1,49024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1690 Å2
ΔGint-6 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.628, 53.458, 70.185
Angle α, β, γ (deg.)90.00, 97.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

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Components

#1: Protein Unsaturated chondroitin disaccharide hydrolase / Unsaturated glucuronyl hydrolase / SagUGL


Mass: 46598.594 Da / Num. of mol.: 1 / Mutation: D115N/K370S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: NEM316 / Gene: gbs1889 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)pLysS
References: UniProt: Q8E372, unsaturated chondroitin disaccharide hydrolase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40% ethylene glycol, 0.1M tris(hydroxymethyl)aminomethane-HCl, 0.5mM dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2013
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 38553 / Num. obs: 35858 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.28 Å2
Reflection shellResolution: 1.79→1.85 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANJ

3anj


Resolution: 1.792→29.056 Å / FOM work R set: 0.8164 / SU ML: 0.19 / σ(F): 1.33 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1786 4.99 %Random
Rwork0.1825 ---
obs0.1839 35816 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.53 Å2 / Biso mean: 29.31 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: LAST / Resolution: 1.792→29.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 48 135 3286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073300
X-RAY DIFFRACTIONf_angle_d1.0154460
X-RAY DIFFRACTIONf_chiral_restr0.076461
X-RAY DIFFRACTIONf_plane_restr0.004571
X-RAY DIFFRACTIONf_dihedral_angle_d14.8661213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7917-1.84010.29381360.23152509264594
1.8401-1.89430.27461220.210326442766100
1.8943-1.95540.23791200.213526472767100
1.9554-2.02530.26911340.202926372771100
2.0253-2.10630.2541440.191526502794100
2.1063-2.20220.21011360.187126062742100
2.2022-2.31820.24931210.186226702791100
2.3182-2.46340.23331450.18832638278399
2.4634-2.65350.20131380.18852636277499
2.6535-2.92030.21961560.17922618277499
2.9203-3.34230.21911510.18772626277799
3.3423-4.20890.191400.17152596273697
4.2089-29.05970.17031430.16842553269693

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