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- PDB-1x1i: Crystal Structure of Xanthan Lyase (N194A) Complexed with a Product -

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Basic information

Entry
Database: PDB / ID: 1x1i
TitleCrystal Structure of Xanthan Lyase (N194A) Complexed with a Product
Componentsxanthan lyase
KeywordsLYASE / alpha/alpha barrel / beta sandwich
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
Chem-46M / Xanthan lyase
Similarity search - Component
Biological speciesBacillus sp. GL1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaruyama, Y. / Hashimoto, W. / Mikami, B. / Murata, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of Bacillus sp. GL1 Xanthan Lyase Complexed with a Substrate: Insights into the Enzyme Reaction Mechanism
Authors: Maruyama, Y. / Hashimoto, W. / Mikami, B. / Murata, K.
History
DepositionApr 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4May 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: xanthan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9642
Polymers80,7131
Non-polymers2501
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.802, 90.677, 77.920
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein xanthan lyase


Mass: 80713.367 Da / Num. of mol.: 1 / Fragment: residues 26-777 / Mutation: N194A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. GL1 (bacteria) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9AQS0, xanthan lyase
#2: Sugar ChemComp-46M / (4AR,6R,7S,8R,8AS)-HEXAHYDRO-6,7,8-TRIHYDROXY-2-METHYLPYRANO[3,2-D][1,3]DIOXINE-2-CARBOXYLIC ACID / [4,6-O-(1-CARBOXYETHYLIDENE)-BETA-D-MANNOSE]


Type: D-saccharide / Mass: 250.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H14O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG4000, Ammonium Formate, Sodium Bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

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: 1.8→50 Å / Num. obs: 68423 / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.078
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.17

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.36 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1616595.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3474 5.1 %RANDOM
Rwork0.176 ---
obs0.176 68222 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0658 Å2 / ksol: 0.322531 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å21.65 Å2
2--0.46 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 17 795 6528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.452
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 571 5.1 %
Rwork0.184 10694 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3pman.param3
X-RAY DIFFRACTION4cis_peptide.param

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