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- PDB-5gmt: Crystal structure of the marine PL-14 alginate lyase from Aplysia... -

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Basic information

Entry
Database: PDB / ID: 5gmt
TitleCrystal structure of the marine PL-14 alginate lyase from Aplysia kurodai
ComponentsAlginate lyase
KeywordsLYASE / alginate lyase / polysaccharide lyase family 14 / glycosidic bond / beta-D-mannuronic acid / alpha-L-guluronic acid
Function / homology: / Polysaccharide lyase 14 / lyase activity / Alginate lyase
Function and homology information
Biological speciesAplysia kurodai (Kuroda's sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsQin, H.-M. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science, and Technology Japan
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14.
Authors: Qin, H.M. / Miyakawa, T. / Inoue, A. / Nishiyama, R. / Nakamura, A. / Asano, A. / Sawano, Y. / Ojima, T. / Tanokura, M.
History
DepositionJul 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)62,3392
Polymers62,3392
Non-polymers00
Water7,530418
1
A: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)31,1701
Polymers31,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)31,1701
Polymers31,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.450, 44.990, 73.020
Angle α, β, γ (deg.)82.57, 88.79, 63.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alginate lyase


Mass: 31169.584 Da / Num. of mol.: 2 / Fragment: UNP residues 29-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia kurodai (Kuroda's sea hare) / Gene: AkAly30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2(DE3)
References: UniProt: E7FLQ2, mannuronate-specific alginate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG3350, Ammonium acetate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 42279 / % possible obs: 94.8 % / Redundancy: 2 % / Rsym value: 0.034 / Net I/σ(I): 17.5
Reflection shellResolution: 1.77→1.82 Å / Rsym value: 0.141

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→36.173 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 18.44
RfactorNum. reflection% reflection
Rfree0.1949 1994 4.72 %
Rwork0.1571 --
obs0.1589 42274 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→36.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4160 0 0 418 4578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074295
X-RAY DIFFRACTIONf_angle_d1.0285791
X-RAY DIFFRACTIONf_dihedral_angle_d12.3511510
X-RAY DIFFRACTIONf_chiral_restr0.041574
X-RAY DIFFRACTIONf_plane_restr0.005752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.81430.26071450.18212880X-RAY DIFFRACTION95
1.8143-1.86340.23521380.16922863X-RAY DIFFRACTION94
1.8634-1.91820.21071390.16722867X-RAY DIFFRACTION94
1.9182-1.98010.22681390.15762835X-RAY DIFFRACTION94
1.9801-2.05090.23281470.16582882X-RAY DIFFRACTION95
2.0509-2.1330.20251410.16342867X-RAY DIFFRACTION94
2.133-2.230.20331330.1582864X-RAY DIFFRACTION95
2.23-2.34760.21421490.15952883X-RAY DIFFRACTION95
2.3476-2.49460.20081460.15892897X-RAY DIFFRACTION96
2.4946-2.68720.18761410.15922890X-RAY DIFFRACTION95
2.6872-2.95750.18051470.1572855X-RAY DIFFRACTION95
2.9575-3.38520.17831440.15062909X-RAY DIFFRACTION95
3.3852-4.26390.16561400.14372882X-RAY DIFFRACTION95
4.2639-36.1810.17911450.15492906X-RAY DIFFRACTION96

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