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- PDB-7xzb: Mutant (Y242A) of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xzb
TitleMutant (Y242A) 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: 2.25 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
B: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6804
Polymers99,4882
Non-polymers1922
Water11,205622
1
A: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8402
Polymers49,7441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8402
Polymers49,7441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.639, 57.746, 88.202
Angle α, β, γ (deg.)90.101, 101.329, 92.089
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Fucoidan lyase


Mass: 49743.949 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: Y242A
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)
Production host: Escherichia coli (E. coli)
References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 58.79 %
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: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→27.67 Å / Num. obs: 46873 / % possible obs: 95.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.06 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 3.3
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 4394 / Rpim(I) all: 0.262 / % possible all: 96.1

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Processing

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

7xzf


Resolution: 2.25→27.67 Å / SU ML: 0.2422 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.3022
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 2304 4.92 %
Rwork0.1855 44493 -
obs0.1871 46797 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.87 Å2
Refinement stepCycle: LAST / Resolution: 2.25→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 0 622 7346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456870
X-RAY DIFFRACTIONf_angle_d0.89199347
X-RAY DIFFRACTIONf_chiral_restr0.06351061
X-RAY DIFFRACTIONf_plane_restr0.00521241
X-RAY DIFFRACTIONf_dihedral_angle_d16.90322461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.27721340.23492399X-RAY DIFFRACTION81.84
2.3-2.360.28731580.20772806X-RAY DIFFRACTION97.18
2.36-2.410.2681490.19952857X-RAY DIFFRACTION97.28
2.41-2.480.27981550.19542764X-RAY DIFFRACTION97.46
2.48-2.550.26971400.19912876X-RAY DIFFRACTION97.04
2.55-2.640.21291270.19482850X-RAY DIFFRACTION97.54
2.64-2.730.27151350.20472770X-RAY DIFFRACTION94.81
2.73-2.840.24121420.19142836X-RAY DIFFRACTION97.42
2.84-2.970.25051400.19352850X-RAY DIFFRACTION97.87
2.97-3.120.22371410.18982813X-RAY DIFFRACTION97.24
3.12-3.320.21091320.18122851X-RAY DIFFRACTION96.79
3.32-3.580.20521820.17542646X-RAY DIFFRACTION92.15
3.58-3.930.17441530.16542737X-RAY DIFFRACTION95.25
3.93-4.50.16121160.15092861X-RAY DIFFRACTION96.41
4.5-5.660.16531410.16392791X-RAY DIFFRACTION96.26
5.66-27.670.22291590.2122786X-RAY DIFFRACTION95.8
Refinement TLS params.Method: refined / Origin x: 58.4448274666 Å / Origin y: -31.1556809277 Å / Origin z: -67.6475156605 Å
111213212223313233
T0.0405815369367 Å20.000556394089839 Å2-0.00564530292977 Å2-0.0424519222306 Å20.00866093487861 Å2--0.0499145152515 Å2
L0.0779297867823 °2-0.0470926150542 °2-0.0815249471402 °2-0.0771373977788 °20.0980044077406 °2--0.218018439506 °2
S-0.0121111332326 Å °-0.00165705794025 Å °0.000358472861974 Å °0.00470076390627 Å °-0.00362572907921 Å °0.00972191086857 Å °0.00103323856383 Å °0.00759538636023 Å °-8.07636996689E-5 Å °
Refinement TLS groupSelection details: all

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