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- PDB-2gh4: YteR/D143N/dGalA-Rha -

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Basic information

Entry
Database: PDB / ID: 2gh4
TitleYteR/D143N/dGalA-Rha
ComponentsPutative glycosyl hydrolase yteR
KeywordsHYDROLASE / alpha / alpha barrel
Function / homology
Function and homology information


unsaturated rhamnogalacturonyl hydrolase / unsaturated rhamnogalacturonyl hydrolase activity / carbohydrate metabolic 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 rhamnogalacturonyl hydrolase YteR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsItoh, T. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate
Authors: Itoh, T. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionMar 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Putative glycosyl hydrolase yteR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3072
Polymers42,0011
Non-polymers3061
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.879, 91.879, 178.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2267-

HOH

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Components

#1: Protein Putative glycosyl hydrolase yteR / unsaturated rhamnogalacturonyl hydrolase


Mass: 42000.543 Da / Num. of mol.: 1 / Fragment: residues 11-373 / Mutation: D143N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: sp.168 / Gene: yteR / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O34559, 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-(1-2)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 306.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2211m-1a_1-5][a21eEA-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(2+1)][a-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 1.2M citrate, 0.1M Tris-HCl, pH 7.5, EVAPORATION, 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: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35001 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.9→1.97 Å / % possible all: 88.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NC5

1nc5


Resolution: 1.9→14.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3292195.11 / 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
Rfree0.233 3464 9.9 %RANDOM
Rwork0.188 ---
obs0.188 34873 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.2607 Å2 / ksol: 0.389502 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å24.2 Å20 Å2
2--3.65 Å20 Å2
3----7.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 22 287 3323
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it3.661.5
X-RAY DIFFRACTIONc_mcangle_it4.152
X-RAY DIFFRACTIONc_scbond_it5.142
X-RAY DIFFRACTIONc_scangle_it6.22.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 514 9.9 %
Rwork0.31 4703 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dgala_rha_pam.txtdgala_rha_top.txt

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