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- PDB-2ahf: Unsaturated glucuronyl hydrolase mutant D88N -

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Basic information

Entry
Database: PDB / ID: 2ahf
TitleUnsaturated glucuronyl hydrolase mutant D88N
Componentsunsaturated glucuronyl hydrolase
KeywordsHYDROLASE / alpha6/alpha6 barrel / glycoside hydrolase family 88
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: 1.52 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
DepositionJul 28, 2005Deposition site: RCSB / 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 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)85,8272
Polymers85,8272
Non-polymers00
Water15,601866
1
A: unsaturated glucuronyl hydrolase


Theoretical massNumber of molelcules
Total (without water)42,9131
Polymers42,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: unsaturated glucuronyl hydrolase


Theoretical massNumber of molelcules
Total (without water)42,9131
Polymers42,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.905, 95.385, 95.285
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: 42913.367 Da / Num. of mol.: 2 / Mutation: D88N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Plasmid: pET3a / 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


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.3 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG10000, 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: 0.8 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 119866 / % possible obs: 97.2 % / Observed criterion σ(I): 631135 / Biso Wilson estimate: 16.8 Å2
Reflection shellResolution: 1.52→1.57 Å / % possible all: 93.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→14.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2128419.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 11983 10 %RANDOM
Rwork0.186 ---
obs0.186 119651 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0969 Å2 / ksol: 0.39392 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2---1.99 Å20 Å2
3---0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.52→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6070 0 0 866 6936
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_d0.74
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it3.552
X-RAY DIFFRACTIONc_scangle_it4.42.5
LS refinement shellResolution: 1.52→1.62 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 1879 9.7 %
Rwork0.271 17395 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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