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- PDB-8jt4: Substrate -binding mode guided protein design of alginate lyase F... -

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Basic information

Entry
Database: PDB / ID: 8jt4
TitleSubstrate -binding mode guided protein design of alginate lyase FlAlyA for altered end-product distribution
ComponentsAlginate lyase
KeywordsLYASE / mutation
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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsZhang, X. / Yang, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31960203 China
CitationJournal: To Be Published
Title: Substrate -binding mode guided protein design of alginate lyase FlAlyA for altered end-product distribution
Authors: Zhang, X. / Yang, D.F.
History
DepositionJun 21, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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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)29,9921
Polymers29,9921
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.998, 71.998, 52.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Alginate lyase


Mass: 29991.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. UMI-01 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A068PC91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.62 Å3/Da / Density % sol: 52.97 % / Description: bulk
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.45→31.18 Å / Num. obs: 53504 / % possible obs: 99.2 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06089 / Net I/σ(I): 15.61
Reflection shellResolution: 1.45→1.502 Å / Rmerge(I) obs: 0.2544 / Num. unique obs: 5184 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
DIALSdata reduction
Aimlessdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→31.18 Å / Cross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1927 --
Rwork0.1598 --
obs-53484 99.2 %
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 232 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072166
X-RAY DIFFRACTIONf_angle_d0.84392928
X-RAY DIFFRACTIONf_chiral_restr0.0853310
X-RAY DIFFRACTIONf_plane_restr0.0069373
X-RAY DIFFRACTIONf_dihedral_angle_d12.63021301

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