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- PDB-5wut: Crystal structure of laminarinase from Flavobacterium sp. UMI-01 -

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Basic information

Entry
Database: PDB / ID: 5wut
TitleCrystal structure of laminarinase from Flavobacterium sp. UMI-01
ComponentsULam111
KeywordsHYDROLASE / laminarinase / glycosidic bond / thermostability / b-jelly roll fold
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsQin, H.M. / Miyakawa, Y. / Nakamura, A. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science, and Technology Japan
CitationJournal: To Be Published
Title: Crystal structure of laminarinase from Flavobacterium sp. UMI-01
Authors: Qin, H.M. / Miyakawa, Y. / Nakamura, A. / Tanokura, M.
History
DepositionDec 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: ULam111
B: ULam111


Theoretical massNumber of molelcules
Total (without water)54,1692
Polymers54,1692
Non-polymers00
Water12,070670
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area19350 Å2
Unit cell
Length a, b, c (Å)64.630, 80.880, 109.490
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 ULam111


Mass: 27084.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1CVU5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium citrate (pH 5.6), 30% (w/v) polyethylene glycol 4000, and 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 76300 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 25.71
Reflection shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 6.6 / % 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: 1.6→40.44 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.83
RfactorNum. reflection% reflection
Rfree0.2059 3833 5.03 %
Rwork0.1758 --
obs0.1773 76276 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 0 670 4418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083868
X-RAY DIFFRACTIONf_angle_d1.185246
X-RAY DIFFRACTIONf_dihedral_angle_d12.9861388
X-RAY DIFFRACTIONf_chiral_restr0.054541
X-RAY DIFFRACTIONf_plane_restr0.006672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62020.21041390.18662676X-RAY DIFFRACTION100
1.6202-1.64160.2361250.192648X-RAY DIFFRACTION100
1.6416-1.6640.21451450.17572622X-RAY DIFFRACTION100
1.664-1.68780.23811440.18612652X-RAY DIFFRACTION100
1.6878-1.7130.22091330.18092668X-RAY DIFFRACTION100
1.713-1.73980.2251460.17662649X-RAY DIFFRACTION100
1.7398-1.76830.24241330.18682680X-RAY DIFFRACTION100
1.7683-1.79880.24321300.18822660X-RAY DIFFRACTION100
1.7988-1.83150.22531290.18432635X-RAY DIFFRACTION100
1.8315-1.86670.21991370.19112672X-RAY DIFFRACTION100
1.8667-1.90480.22321270.1872702X-RAY DIFFRACTION100
1.9048-1.94620.22831470.18312646X-RAY DIFFRACTION100
1.9462-1.99150.21271450.17832663X-RAY DIFFRACTION100
1.9915-2.04130.21071420.17082679X-RAY DIFFRACTION100
2.0413-2.09650.19131480.17842667X-RAY DIFFRACTION100
2.0965-2.15820.19731440.17712680X-RAY DIFFRACTION100
2.1582-2.22790.21541490.17682662X-RAY DIFFRACTION100
2.2279-2.30750.22661400.18222686X-RAY DIFFRACTION100
2.3075-2.39980.21331280.18092686X-RAY DIFFRACTION100
2.3998-2.50910.22391440.18652683X-RAY DIFFRACTION100
2.5091-2.64130.18091460.1832694X-RAY DIFFRACTION100
2.6413-2.80680.1971490.18652696X-RAY DIFFRACTION100
2.8068-3.02340.22891600.192696X-RAY DIFFRACTION100
3.0234-3.32750.21331500.17712704X-RAY DIFFRACTION100
3.3275-3.80870.1951490.16242740X-RAY DIFFRACTION100
3.8087-4.79740.15461580.14022739X-RAY DIFFRACTION100
4.7974-40.45290.19821460.17522858X-RAY DIFFRACTION98

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