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- PDB-7xzf: Wild type of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xzf
TitleWild type 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 / SAD / Resolution: 1.3 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 1.1May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / 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)101,60814
Polymers100,5132
Non-polymers1,09512
Water17,330962
1
A: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8027
Polymers50,2561
Non-polymers5456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16730 Å2
MethodPISA
2
B: Fucoidan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8067
Polymers50,2561
Non-polymers5496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-14 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.001, 58.172, 88.319
Angle α, β, γ (deg.)90.266, 101.603, 92.008
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: 50256.434 Da / Num. of mol.: 2 / Fragment: N-terminal domain
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.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M CAPS pH 10.5, 0.2M Lithium sulfate, 2M ammonium sulfate
PH range: 7.5-10.5

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 290039 / % possible obs: 94.8 % / Redundancy: 2 % / Biso Wilson estimate: 8.82 Å2 / Rrim(I) all: 0.113 / Net I/σ(I): 8.9
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 13327 / Rpim(I) all: 0.505

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→24.99 Å / SU ML: 0.1097 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 14.9068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1576 12220 4.96 %
Rwork0.1358 233910 -
obs0.1369 246130 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.94 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 35 962 7763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147425
X-RAY DIFFRACTIONf_angle_d1.404710190
X-RAY DIFFRACTIONf_chiral_restr0.11691134
X-RAY DIFFRACTIONf_plane_restr0.00881381
X-RAY DIFFRACTIONf_dihedral_angle_d17.75762689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.2423680.21367599X-RAY DIFFRACTION92.65
1.31-1.330.23373790.20367571X-RAY DIFFRACTION92.65
1.33-1.350.20224070.19517673X-RAY DIFFRACTION92.87
1.35-1.360.21484020.18697546X-RAY DIFFRACTION92.94
1.36-1.380.23124170.18367679X-RAY DIFFRACTION92.97
1.38-1.40.20124340.16867574X-RAY DIFFRACTION93.41
1.4-1.420.21234020.16297762X-RAY DIFFRACTION93.56
1.42-1.440.18564200.15237598X-RAY DIFFRACTION93.68
1.44-1.460.18463790.14567757X-RAY DIFFRACTION93.96
1.46-1.490.17453630.13777735X-RAY DIFFRACTION94.05
1.49-1.510.16874120.12767692X-RAY DIFFRACTION94.34
1.51-1.540.16834080.12657780X-RAY DIFFRACTION94.38
1.54-1.570.16013780.12367756X-RAY DIFFRACTION94.58
1.57-1.60.1554080.11537773X-RAY DIFFRACTION94.81
1.6-1.640.14983980.11277828X-RAY DIFFRACTION95.12
1.64-1.680.15254220.11287809X-RAY DIFFRACTION95.15
1.68-1.720.15294180.11097785X-RAY DIFFRACTION95.56
1.72-1.760.14444460.11447817X-RAY DIFFRACTION95.57
1.76-1.820.1343910.11147874X-RAY DIFFRACTION95.72
1.82-1.870.15044030.11637876X-RAY DIFFRACTION96.07
1.87-1.940.14154290.1197865X-RAY DIFFRACTION96.05
1.94-2.020.14814270.11947890X-RAY DIFFRACTION96.31
2.02-2.110.1554220.11967869X-RAY DIFFRACTION96.37
2.11-2.220.1444590.12167858X-RAY DIFFRACTION96.25
2.22-2.360.14594000.12547922X-RAY DIFFRACTION96.25
2.36-2.540.15564010.13237766X-RAY DIFFRACTION94.5
2.54-2.80.15774280.1427896X-RAY DIFFRACTION96.86
2.8-3.20.14693940.14888120X-RAY DIFFRACTION98.63
3.2-4.030.14633970.13718133X-RAY DIFFRACTION98.91
4.03-24.990.14364080.14728107X-RAY DIFFRACTION98.64

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