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- PDB-5y33: Crystal structure of alginate lyase from Flavobacterium sp. UMI-0... -

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Basic information

Entry
Database: PDB / ID: 5y33
TitleCrystal structure of alginate lyase from Flavobacterium sp. UMI-01 reveals polymannuronate specificity
ComponentsAlginate lyase
KeywordsSTRUCTURAL PROTEIN / alginate lyase / b-elimination reaction / b-jelly roll fold / endolytic enzyme
Function / homologyAlginate lyase 2 / Alginate lyase / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / lyase activity / Alginate lyase
Function and homology information
Biological speciesFlavobacterium sp. UMI-01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsQin, H.-M. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Structural basis for controlling the enzymatic properties of polymannuronate preferred alginate lyase FlAlyA from the PL-7 family.
Authors: Qin, H.M. / Miyakawa, T. / Inoue, A. / Nishiyama, R. / Nakamura, A. / Asano, A. / Ojima, T. / Tanokura, M.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)29,9021
Polymers29,9021
Non-polymers00
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12080 Å2
Unit cell
Length a, b, c (Å)71.750, 71.750, 50.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Alginate lyase


Mass: 29901.758 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. UMI-01 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A068PC91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 43349 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.039 / Net I/σ(I): 38.5
Reflection shellResolution: 1.54→1.58 Å / Rsym value: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHENIXdata reduction
PHENIXdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.54→31.069 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 19.71
RfactorNum. reflection% reflection
Rfree0.1929 4304 9.93 %
Rwork0.1656 --
obs0.1683 43342 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.54→31.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 0 340 2446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172159
X-RAY DIFFRACTIONf_angle_d1.7022918
X-RAY DIFFRACTIONf_dihedral_angle_d13.167809
X-RAY DIFFRACTIONf_chiral_restr0.076307
X-RAY DIFFRACTIONf_plane_restr0.01372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5399-1.55740.24261410.19451295X-RAY DIFFRACTION99
1.5574-1.57570.23931390.19221312X-RAY DIFFRACTION100
1.5757-1.5950.24551570.18771310X-RAY DIFFRACTION100
1.595-1.61510.22861530.18941241X-RAY DIFFRACTION100
1.6151-1.63640.23351490.18131355X-RAY DIFFRACTION100
1.6364-1.65880.21751230.18351303X-RAY DIFFRACTION100
1.6588-1.68250.23751350.19241282X-RAY DIFFRACTION100
1.6825-1.70760.23741390.19331310X-RAY DIFFRACTION100
1.7076-1.73430.24721430.19631280X-RAY DIFFRACTION100
1.7343-1.76270.22461270.19411323X-RAY DIFFRACTION100
1.7627-1.79310.20361510.18081336X-RAY DIFFRACTION100
1.7931-1.82570.19611310.18221297X-RAY DIFFRACTION100
1.8257-1.86080.24031510.1871290X-RAY DIFFRACTION100
1.8608-1.89880.22341480.18281261X-RAY DIFFRACTION100
1.8988-1.94010.1961280.17941360X-RAY DIFFRACTION100
1.9401-1.98520.22841380.18491297X-RAY DIFFRACTION100
1.9852-2.03490.19911560.17111310X-RAY DIFFRACTION100
2.0349-2.08990.19471490.17081282X-RAY DIFFRACTION100
2.0899-2.15140.22271330.16991296X-RAY DIFFRACTION100
2.1514-2.22080.19091360.17361317X-RAY DIFFRACTION100
2.2208-2.30010.20691510.17331304X-RAY DIFFRACTION100
2.3001-2.39220.22181500.16821295X-RAY DIFFRACTION100
2.3922-2.5010.20871570.1811283X-RAY DIFFRACTION100
2.501-2.63280.20671520.18441296X-RAY DIFFRACTION100
2.6328-2.79770.20751440.17811292X-RAY DIFFRACTION100
2.7977-3.01350.19111450.18031317X-RAY DIFFRACTION100
3.0135-3.31650.19271500.16461267X-RAY DIFFRACTION100
3.3165-3.79560.16091440.13671320X-RAY DIFFRACTION100
3.7956-4.77930.13241360.12071321X-RAY DIFFRACTION100
4.7793-31.0750.14691480.1411286X-RAY DIFFRACTION100

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