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- PDB-2fuz: UGL hexagonal crystal structure without glycine and DTT molecules -

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Basic information

Entry
Database: PDB / ID: 2fuz
TitleUGL hexagonal crystal structure without glycine and DTT molecules
ComponentsUnsaturated glucuronyl hydrolase
KeywordsHYDROLASE / alpha6/alpha6-barrel
Function / homology
Function and homology information


gellan tetrasaccharide unsaturated glucuronosyl hydrolase / chondroitin hydrolase activity / polysaccharide catabolic process / cytoplasm
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 glucuronyl hydrolase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsItoh, T. / Hashimoto, W. / Mikami, B. / Murata, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1
Authors: Itoh, T. / Hashimoto, W. / Mikami, B. / Murata, K.
History
DepositionJan 28, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 glucuronyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,97810
Polymers42,9141
Non-polymers1,0649
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.818, 102.818, 223.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Unsaturated glucuronyl hydrolase / UGL / Glycuronidase / Unsaturated uronic acid hydrolase / Glycosaminoglycan hydrolase


Mass: 42914.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Gene: ugl / Plasmid: pET3a_UGL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9RC92, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50% MPD, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 64105 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.308 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VD5

1vd5


Resolution: 1.8→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 589626.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.188 6468 10.1 %RANDOM
Rwork0.167 ---
obs0.167 63925 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.3322 Å2 / ksol: 0.357016 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å21.74 Å20 Å2
2--1.55 Å20 Å2
3----3.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 72 396 3503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.681.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it4.132
X-RAY DIFFRACTIONc_scangle_it5.342.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 984 9.4 %
Rwork0.238 9518 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4mpd_xplor_par.txtmpd_xplor_top.txt

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