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- PDB-2e24: crystal structure of a mutant (R612A) of xanthan lyase -

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Basic information

Entry
Database: PDB / ID: 2.0E+24
Titlecrystal structure of a mutant (R612A) of xanthan lyase
ComponentsXanthan lyase
KeywordsLYASE / xanthan / polysaccharide lyase
Function / homology
Function and homology information


xanthan lyase / xanthan lyase activity / polysaccharide metabolic process / D-mannose binding / calcium ion binding / extracellular region
Similarity search - Function
CBM6/CBM35/CBM36-like 2 / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase ...CBM6/CBM35/CBM36-like 2 / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Xanthan lyase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMaruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: Biochemistry / Year: 2007
Title: A Structural Factor Responsible for Substrate Recognition by Bacillus sp. GL1 Xanthan Lyase that Acts Specifically on Pyruvated Side Chains of Xanthan
Authors: Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionNov 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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: Xanthan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7762
Polymers80,6701
Non-polymers1061
Water10,070559
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.807, 90.230, 78.098
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Xanthan lyase /


Mass: 80670.273 Da / Num. of mol.: 1 / Fragment: residues 26-777 / Mutation: R612A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9AQS0, xanthan lyase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 22% PEG 4000, 0.2M ammonium formate, 0.1M Sodium Bicine, pH 9, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 39353 / % possible obs: 97.3 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.113
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.324 / % possible all: 77.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X1H

1x1h


Resolution: 2.15→46.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1639408.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1967 5 %RANDOM
Rwork0.175 ---
obs0.175 39238 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8617 Å2 / ksol: 0.355376 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å23.16 Å2
2---2.02 Å20 Å2
3---2.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.15→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 7 559 6255
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_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 2.15→2.23 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2384 164 4.1 %
Rwork0.2073 2972 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4peg.parampeg.top
X-RAY DIFFRACTION5cis_peptide.param

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