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- PDB-7xz8: Mutant (K141A) of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xz8
TitleMutant (K141A) of the N-terminal domain of fucoidan lyase FdlA
ComponentsFucoidan lyase
KeywordsLYASE / Fucobacter marina / fucoidan lyase / polysaccharide lyase
Biological speciesFlavobacteriaceae bacterium SA-0082 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsWang, J. / Li, M. / Pan, X.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)21877114 China
National Natural Science Foundation of China (NSFC)31930064 China
CitationJournal: Mar Drugs / Year: 2022
Title: Structural and Biochemical Analysis Reveals Catalytic Mechanism of Fucoidan Lyase from Flavobacterium sp. SA-0082.
Authors: Wang, J. / Liu, Z. / Pan, X. / Wang, N. / Li, L. / Du, Y. / Li, J. / Li, M.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucoidan lyase


Theoretical massNumber of molelcules
Total (without water)50,1981
Polymers50,1981
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16700 Å2
Unit cell
Length a, b, c (Å)90.480, 90.480, 123.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Fucoidan lyase


Mass: 50198.332 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: K141A
Source method: isolated from a genetically manipulated source
Details: Genbank AAO00510.1,Sequence 3 from patent US 6489155
Source: (gene. exp.) Flavobacteriaceae bacterium SA-0082 (bacteria)
Gene: AAO5510.1 / Production host: Escherichia (bacteria)
References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS, pH 10.5, 0.2 M lithium sulfate, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→30.47 Å / Num. obs: 45444 / % possible obs: 99.1 % / Redundancy: 19.9 % / Biso Wilson estimate: 34.93 Å2 / Rrim(I) all: 0.063 / Net I/σ(I): 24.4
Reflection shellResolution: 1.89→1.93 Å / Num. unique obs: 2495 / Rrim(I) all: 0.078

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZXF

7zxf


Resolution: 1.89→22.62 Å / SU ML: 0.2702 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.8252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 2198 4.84 %
Rwork0.1797 43235 -
obs0.1813 45433 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.46 Å2
Refinement stepCycle: LAST / Resolution: 1.89→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 274 3640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743483
X-RAY DIFFRACTIONf_angle_d0.92084745
X-RAY DIFFRACTIONf_chiral_restr0.0604535
X-RAY DIFFRACTIONf_plane_restr0.0048635
X-RAY DIFFRACTIONf_dihedral_angle_d16.7821253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.930.40781250.34372492X-RAY DIFFRACTION91.41
1.93-1.980.30831120.29562634X-RAY DIFFRACTION96.25
1.98-2.030.31351440.27012680X-RAY DIFFRACTION99.16
2.03-2.080.2921300.26472694X-RAY DIFFRACTION99.96
2.08-2.140.3021260.24172764X-RAY DIFFRACTION100
2.14-2.210.25181320.2222731X-RAY DIFFRACTION100
2.21-2.290.24621370.21872705X-RAY DIFFRACTION100
2.29-2.380.27061470.21342725X-RAY DIFFRACTION100
2.38-2.490.24311630.2112675X-RAY DIFFRACTION100
2.49-2.620.25831410.1992701X-RAY DIFFRACTION100
2.62-2.780.24911210.19382752X-RAY DIFFRACTION100
2.78-30.22991290.19182757X-RAY DIFFRACTION100
3-3.30.22191210.1832726X-RAY DIFFRACTION100
3.3-3.770.20081730.15982715X-RAY DIFFRACTION100
3.77-4.750.16071550.13242729X-RAY DIFFRACTION100
4.75-22.620.1661420.14872755X-RAY DIFFRACTION99.72

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