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- PDB-1uai: Crystal Structure of the Alginate Lyase from Corynebacterium sp. -

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Basic information

Entry
Database: PDB / ID: 1uai
TitleCrystal Structure of the Alginate Lyase from Corynebacterium sp.
Componentspolyguluronate lyase
KeywordsLYASE / jellyroll beta-sandwich
Function / homology
Function and homology information


guluronate-specific alginate lyase / poly(alpha-L-guluronate) lyase activity
Similarity search - Function
Alginate lyase 2 / Alginate lyase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Polyguluronate lyase
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKakuta, Y.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution
Authors: Osawa, T. / Matsubara, Y. / Muramatsu, T. / Kimura, M. / Kakuta, Y.
History
DepositionMar 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: polyguluronate lyase


Theoretical massNumber of molelcules
Total (without water)24,3411
Polymers24,3411
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.925, 47.234, 50.307
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein polyguluronate lyase / Alginate Lyase


Mass: 24340.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Corynebacterium sp. (bacteria)
References: UniProt: Q9RB42, guluronate-specific alginate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→35 Å / Num. obs: 59499 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.1
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 13.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→34.44 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 656713.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2982 5 %RANDOM
Rwork0.17 ---
obs0.17 59170 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0767 Å2 / ksol: 0.393406 e/Å3
Displacement parametersBiso mean: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.05 Å2
2--0.19 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.2→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 0 346 2055
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.2→1.28 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.182 456 4.8 %
Rwork0.178 9005 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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