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- PDB-7xzc: Mutant (R240A) of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xzc
TitleMutant (R240A) 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: 1.7 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


Theoretical massNumber of molelcules
Total (without water)100,3412
Polymers100,3412
Non-polymers00
Water13,061725
1
A: Fucoidan lyase


Theoretical massNumber of molelcules
Total (without water)50,1701
Polymers50,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucoidan lyase


Theoretical massNumber of molelcules
Total (without water)50,1701
Polymers50,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.798, 57.972, 88.150
Angle α, β, γ (deg.)90.228, 78.683, 87.861
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: 50170.316 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: R240A
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.: 725 / 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: 2.78 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 10% (v/v) 2-Propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 107712 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.93 Å2 / Rrim(I) all: 0.09 / Net I/σ(I): 7.2
Reflection shellResolution: 1.69→1.77 Å / Num. unique obs: 5947 / Rrim(I) all: 0.66 / % possible all: 94.7

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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: 1.7→47.86 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.2534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1918 5460 5.07 %
Rwork0.1635 102213 -
obs0.1649 107673 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 0 725 7447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01186971
X-RAY DIFFRACTIONf_angle_d1.09239501
X-RAY DIFFRACTIONf_chiral_restr0.07961073
X-RAY DIFFRACTIONf_plane_restr0.00611271
X-RAY DIFFRACTIONf_dihedral_angle_d16.77692507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.2711050.22912252X-RAY DIFFRACTION61.44
1.72-1.740.27541210.22592477X-RAY DIFFRACTION67.85
1.74-1.760.25821610.22022718X-RAY DIFFRACTION75.45
1.76-1.780.27051500.20533276X-RAY DIFFRACTION89.8
1.78-1.810.25841970.20063459X-RAY DIFFRACTION95.11
1.81-1.830.23211780.18933467X-RAY DIFFRACTION95.8
1.83-1.860.23161930.18293524X-RAY DIFFRACTION96.07
1.86-1.890.19082020.17563450X-RAY DIFFRACTION96.31
1.89-1.910.20241990.18143535X-RAY DIFFRACTION96.24
1.91-1.950.21122190.17493414X-RAY DIFFRACTION96.21
1.95-1.980.21781790.17193484X-RAY DIFFRACTION96.22
1.98-2.020.22221930.16883507X-RAY DIFFRACTION96.13
2.02-2.050.19651920.173508X-RAY DIFFRACTION96.5
2.05-2.10.19911880.16543502X-RAY DIFFRACTION96.62
2.1-2.140.19051830.16743564X-RAY DIFFRACTION96.8
2.14-2.190.18571940.15783487X-RAY DIFFRACTION96.77
2.19-2.250.18192070.16483516X-RAY DIFFRACTION97.16
2.25-2.310.20931860.16543516X-RAY DIFFRACTION96.94
2.31-2.380.21191540.16743544X-RAY DIFFRACTION97.11
2.38-2.450.1951940.17253555X-RAY DIFFRACTION97
2.45-2.540.19221790.17143538X-RAY DIFFRACTION97.05
2.54-2.640.22471880.17233520X-RAY DIFFRACTION97.48
2.64-2.760.19372030.17473542X-RAY DIFFRACTION97.58
2.76-2.910.22721830.17593525X-RAY DIFFRACTION97.45
2.91-3.090.20141990.17533551X-RAY DIFFRACTION97.73
3.09-3.330.17812060.16133473X-RAY DIFFRACTION96.28
3.33-3.660.17011950.14413563X-RAY DIFFRACTION98.12
3.66-4.190.14431480.13433601X-RAY DIFFRACTION97.81
4.19-5.280.13511780.12923564X-RAY DIFFRACTION97.63
5.28-47.860.19041860.16473581X-RAY DIFFRACTION98.54

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