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- PDB-8jsd: Alginate lyase mutant-D180G -

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Basic information

Entry
Database: PDB / ID: 8jsd
TitleAlginate lyase mutant-D180G
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: 1.414 Å
AuthorsZhang, X. / Pan, L.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. / Pan, L.X.
History
DepositionJun 19, 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)29,9571
Polymers29,9571
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.120, 72.120, 52.060
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: 29956.881 Da / Num. of mol.: 1 / Mutation: D180G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. UMI-01 (bacteria) / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: A0A068PC91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.64 Å3/Da / Density % sol: 53.1 % / 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: 1.414→31.23 Å / Num. obs: 55650 / % possible obs: 96.11 % / Redundancy: 8.9 % / Biso Wilson estimate: 20.69 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04724 / Rpim(I) all: 0.0159 / Rrim(I) all: 0.04989 / Net I/σ(I): 22.74
Reflection shellResolution: 1.414→1.465 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.4322 / Num. unique obs: 5177 / CC1/2: 0.914 / CC star: 0.977 / Rpim(I) all: 0.2143 / Rrim(I) all: 0.4858 / % possible all: 89.86

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
autoPROCdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.414→31.23 Å / Cross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1676 --
Rwork0.141 --
obs-55650 96.11 %
Refinement stepCycle: LAST / Resolution: 1.414→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 0 302 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732165
X-RAY DIFFRACTIONf_angle_d1.0362926
X-RAY DIFFRACTIONf_chiral_restr0.0823309
X-RAY DIFFRACTIONf_plane_restr0.0076372
X-RAY DIFFRACTIONf_dihedral_angle_d13.9261297

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