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- PDB-7xze: Mutant (H176A) of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xze
TitleMutant (H176A) of the N-terminal domain of fucoidan lyase FdlA
ComponentsFucoidan lyase
KeywordsLYASE / Fucobacter marina / fucoidan lyase / polysaccharide lyase
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesFlavobacteriaceae bacterium SA-0082 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)100,7366
Polymers100,3792
Non-polymers3574
Water15,979887
1
A: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3553
Polymers50,1891
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area16610 Å2
MethodPISA
2
B: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3813
Polymers50,1891
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.017, 58.179, 88.537
Angle α, β, γ (deg.)90.269, 101.410, 92.191
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: 50189.363 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: H176A
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M CAPS, pH10.5, 0.2M lithium sulfate, 2M 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: Dec 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→58 Å / Num. obs: 91221 / % possible obs: 92.5 % / Redundancy: 6 % / Biso Wilson estimate: 17.85 Å2 / Rrim(I) all: 0.07 / Net I/σ(I): 24.3
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 6539 / Rrim(I) all: 0.91

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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: 7XZF

7xzf


Resolution: 1.8→52.91 Å / SU ML: 0.1949 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.9655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1894 4383 4.81 %
Rwork0.1581 86810 -
obs0.1596 91196 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 20 887 7637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01366969
X-RAY DIFFRACTIONf_angle_d1.12039490
X-RAY DIFFRACTIONf_chiral_restr0.08741069
X-RAY DIFFRACTIONf_plane_restr0.00591266
X-RAY DIFFRACTIONf_dihedral_angle_d18.2812505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.3041670.27342848X-RAY DIFFRACTION92.34
1.82-1.840.28671790.25172913X-RAY DIFFRACTION95.02
1.84-1.860.27331770.23722952X-RAY DIFFRACTION94.19
1.86-1.880.24781410.21352969X-RAY DIFFRACTION94.1
1.88-1.910.23321500.2032867X-RAY DIFFRACTION93.78
1.91-1.930.23991600.19393019X-RAY DIFFRACTION94.44
1.93-1.960.22431440.17462933X-RAY DIFFRACTION94.18
1.96-1.990.21570.16722914X-RAY DIFFRACTION93.71
1.99-2.020.18171390.16432937X-RAY DIFFRACTION93.98
2.02-2.060.21131510.16032928X-RAY DIFFRACTION93.64
2.06-2.090.19841200.16362965X-RAY DIFFRACTION93.12
2.09-2.130.19821100.15842946X-RAY DIFFRACTION93.2
2.13-2.170.19791450.15772917X-RAY DIFFRACTION92.82
2.17-2.210.19471390.15392824X-RAY DIFFRACTION91.51
2.21-2.260.20641360.1542919X-RAY DIFFRACTION91.69
2.26-2.310.16481380.1532827X-RAY DIFFRACTION90.51
2.31-2.370.19891410.15032793X-RAY DIFFRACTION89.1
2.37-2.440.18111570.15482708X-RAY DIFFRACTION86.79
2.44-2.510.2021130.15492437X-RAY DIFFRACTION77.86
2.51-2.590.18931470.15982758X-RAY DIFFRACTION88.62
2.59-2.680.20991530.15963017X-RAY DIFFRACTION95.34
2.68-2.790.24221500.15763014X-RAY DIFFRACTION96.38
2.79-2.920.18751440.15372996X-RAY DIFFRACTION96.44
2.92-3.070.18981350.15863000X-RAY DIFFRACTION95.67
3.07-3.260.18091780.1422983X-RAY DIFFRACTION95.53
3.26-3.510.17211630.14242927X-RAY DIFFRACTION93.98
3.51-3.870.15661460.1272935X-RAY DIFFRACTION93.36
3.87-4.430.15091370.12682780X-RAY DIFFRACTION89.2
4.43-5.580.13241280.1412687X-RAY DIFFRACTION85.72
5.58-52.910.18641380.18963097X-RAY DIFFRACTION98.15

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