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- PDB-2d5j: Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ethe... -

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Basic information

Entry
Database: PDB / ID: 2d5j
TitleUnsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ether Group but not of Glycosidic Bond
Componentsunsaturated glucuronyl hydrolase
KeywordsHYDROLASE / alpha/alpha barrel / unsaturated glucuronyl hydrolase
Function / homology
Function and homology information


gellan tetrasaccharide unsaturated glucuronosyl hydrolase / hydrolase activity, acting on glycosyl bonds / 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: 1.6 Å
AuthorsItoh, T. / Hashimoto, W. / Mikami, B. / Murata, K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of Unsaturated Glucuronyl Hydrolase Complexed with Substrate: MOLECULAR INSIGHTS INTO ITS CATALYTIC REACTION MECHANISM
Authors: Itoh, T. / Hashimoto, W. / Mikami, B. / Murata, K.
History
DepositionNov 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: unsaturated glucuronyl hydrolase
B: unsaturated glucuronyl hydrolase


Theoretical massNumber of molelcules
Total (without water)85,8292
Polymers85,8292
Non-polymers00
Water15,043835
1
A: unsaturated glucuronyl hydrolase


Theoretical massNumber of molelcules
Total (without water)42,9141
Polymers42,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: unsaturated glucuronyl hydrolase


Theoretical massNumber of molelcules
Total (without water)42,9141
Polymers42,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.000, 95.321, 95.326
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 unsaturated glucuronyl hydrolase


Mass: 42914.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 30% PEG10000, 0.15M Tris pH 8.6, 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: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 93414 / % possible obs: 87.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.276 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→9.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1726790.34 / 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
Rfree0.22 9245 10 %RANDOM
Rwork0.186 ---
obs0.186 92660 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.697 Å2 / ksol: 0.451516 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---1.27 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6070 0 0 835 6905
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.361.5
X-RAY DIFFRACTIONc_mcangle_it2.932
X-RAY DIFFRACTIONc_scbond_it3.842
X-RAY DIFFRACTIONc_scangle_it4.612.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 1702 10.1 %
Rwork0.242 15105 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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