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- PDB-7xz7: Mutant (D137A) of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xz7
TitleMutant (D137A) 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: 1.98 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)100,4252
Polymers100,4252
Non-polymers00
Water11,890660
1
A: Fucoidan lyase


Theoretical massNumber of molelcules
Total (without water)50,2121
Polymers50,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucoidan lyase


Theoretical massNumber of molelcules
Total (without water)50,2121
Polymers50,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.551, 58.386, 88.287
Angle α, β, γ (deg.)90.165, 101.917, 92.251
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: 50212.422 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: D137A
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 coli (E. coli)
References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, pH8.5, 0.2M Li2SO4, 30% (w/v) polyethylene glycol (PEG) 4000
PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→58.33 Å / Num. obs: 67747 / % possible obs: 90.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.54 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Net I/σ(I): 6.7
Reflection shellResolution: 1.98→2 Å / Rmerge(I) obs: 0.889 / Num. unique obs: 2754 / % possible all: 92

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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: 1.98→58.33 Å / SU ML: 0.1922 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1975 3429 5.06 %
Rwork0.1561 64298 -
obs0.1582 67726 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.53 Å2
Refinement stepCycle: LAST / Resolution: 1.98→58.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 0 660 7366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01766830
X-RAY DIFFRACTIONf_angle_d1.44849286
X-RAY DIFFRACTIONf_chiral_restr0.09551054
X-RAY DIFFRACTIONf_plane_restr0.00881230
X-RAY DIFFRACTIONf_dihedral_angle_d18.56672446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.25461470.21482754X-RAY DIFFRACTION91.92
2.01-2.040.23781730.20152684X-RAY DIFFRACTION92.4
2.04-2.070.24061270.19172718X-RAY DIFFRACTION92.07
2.07-2.10.24951280.19582725X-RAY DIFFRACTION91.82
2.1-2.140.24851370.17432687X-RAY DIFFRACTION92.17
2.14-2.180.25251310.18352774X-RAY DIFFRACTION91.55
2.18-2.220.2171160.17432605X-RAY DIFFRACTION89.86
2.22-2.260.23791330.16882672X-RAY DIFFRACTION88.71
2.26-2.310.23931290.17072590X-RAY DIFFRACTION89.32
2.31-2.370.24181340.16662492X-RAY DIFFRACTION83.66
2.37-2.430.21091350.16292431X-RAY DIFFRACTION83.18
2.43-2.490.23161710.15932764X-RAY DIFFRACTION94.46
2.49-2.560.20531460.15872759X-RAY DIFFRACTION93.74
2.56-2.650.23541530.1682767X-RAY DIFFRACTION93.53
2.65-2.740.22411450.16342730X-RAY DIFFRACTION93.5
2.74-2.850.23111700.16392734X-RAY DIFFRACTION93.23
2.85-2.980.21521500.16532721X-RAY DIFFRACTION92.97
2.98-3.140.20831400.17232710X-RAY DIFFRACTION91.17
3.14-3.330.20241420.1622542X-RAY DIFFRACTION87.63
3.33-3.590.20951320.14822470X-RAY DIFFRACTION83.34
3.59-3.950.1791620.1342826X-RAY DIFFRACTION96.05
3.95-4.520.14671360.1232824X-RAY DIFFRACTION94.99
4.52-5.690.14331390.1312677X-RAY DIFFRACTION91.67
5.69-6.10.14711530.14712642X-RAY DIFFRACTION89.64
Refinement TLS params.Method: refined / Origin x: 58.4511469856 Å / Origin y: -31.3489968024 Å / Origin z: -67.5232939394 Å
111213212223313233
T0.168803237218 Å2-0.0011460552482 Å2-0.0130418372209 Å2-0.179196227769 Å20.0146049901958 Å2--0.190967337795 Å2
L0.128654188004 °2-0.0988085793507 °2-0.148861496376 °2-0.261148976962 °20.243638058416 °2--0.546077292629 °2
S-0.0133035493675 Å °-0.000304404507258 Å °-0.00838566272758 Å °0.0214358950488 Å °-0.0229122758674 Å °0.0119123284682 Å °0.0370517939956 Å °0.00219510228418 Å °3.8042949618E-12 Å °
Refinement TLS groupSelection details: all

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