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- PDB-2cws: Crystal structure at 1.0 A of alginate lyase A1-II', a member of ... -

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Basic information

Entry
Database: PDB / ID: 2cws
TitleCrystal structure at 1.0 A of alginate lyase A1-II', a member of polysaccharide lyase family-7
Componentsalginate lyase A1-II'
KeywordsLYASE / alginate lyase / polysaccharide lyase family-7
Function / homology
Function and homology information


Alginate lyase 2 / Alginate lyase / Jelly Rolls - #200 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
AuthorsYamasaki, M. / Ogura, K. / Hashimoto, W. / Mikami, B. / Murata, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A Structural Basis for Depolymerization of Alginate by Polysaccharide Lyase Family-7
Authors: Yamasaki, M. / Ogura, K. / Hashimoto, W. / Mikami, B. / Murata, K.
History
DepositionJun 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alginate lyase A1-II'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2094
Polymers25,9251
Non-polymers2843
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.575, 68.473, 80.331
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 alginate lyase A1-II'


Mass: 25924.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q75WP3, mannuronate-specific alginate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 1.66 Å3/Da / Density % sol: 25.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: PEG8000, ammonium sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 99115 / % possible obs: 96 % / Redundancy: 9.29 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.5
Reflection shellResolution: 1→1.04 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5.89 / Num. unique all: 258030 / Rsym value: 0.213 / % possible all: 76

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→10 Å / Num. parameters: 20533 / Num. restraintsaints: 25643 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.134 4942 5.3 %RANDOM
Rwork0.103 ---
all-98931 --
obs-93989 --
Refine analyzeNum. disordered residues: 63 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2140.5
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 16 411 2162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0364
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.103
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.045
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0.078
LS refinement shellResolution: 1→1.04 Å
RfactorNum. reflection% reflection
Rwork0.097 --
obs-7895 72.15 %

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