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- PDB-2fv1: UGL_D88N/dGlcA-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 2fv1
TitleUGL_D88N/dGlcA-GlcNAc
ComponentsUnsaturated glucuronyl hydrolase
KeywordsHYDROLASE / alpha6/alpha6-barrel
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: 1.73 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5534
Polymers85,8272
Non-polymers7272
Water14,214789
1
A: Unsaturated glucuronyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2772
Polymers42,9131
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Unsaturated glucuronyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2772
Polymers42,9131
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.735, 94.890, 95.410
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 / UGL / Glycuronidase / Unsaturated uronic acid hydrolase / Glycosaminoglycan hydrolase


Mass: 42913.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Gene: ugl / Plasmid: pET3a_UGL_D88N / 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: Polysaccharide 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 363.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 25% PEG10000, 0.15M Tris-HCl 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: Dec 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 79850 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.333 / Num. unique all: 6526 / % possible all: 78.9

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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: 1.73→14.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2321746.55 / 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
Rfree0.212 7994 10 %RANDOM
Rwork0.179 ---
obs0.179 79669 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.6395 Å2 / ksol: 0.386637 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2--0.02 Å20 Å2
3----1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.73→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6070 0 52 789 6911
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_it2.641.5
X-RAY DIFFRACTIONc_mcangle_it3.292
X-RAY DIFFRACTIONc_scbond_it4.132
X-RAY DIFFRACTIONc_scangle_it5.112.5
LS refinement shellResolution: 1.73→1.84 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 1187 10.2 %
Rwork0.24 10435 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dhya_drg_pam.txtdhya_drg_top.txt

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