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- PDB-7xza: Mutant (Y242F) of the N-terminal domain of fucoidan lyase FdlA -

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Basic information

Entry
Database: PDB / ID: 7xza
TitleMutant (Y242F) of the N-terminal domain of fucoidan lyase FdlA
ComponentsFucoidan lyase FdlA
KeywordsLYASE / Fucobacter marina / fucoidan lyase / polysaccharide lyase
Biological speciesFlavobacteriaceae bacterium SA-0082 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 FdlA
B: Fucoidan lyase FdlA


Theoretical massNumber of molelcules
Total (without water)100,4812
Polymers100,4812
Non-polymers00
Water10,485582
1
A: Fucoidan lyase FdlA


Theoretical massNumber of molelcules
Total (without water)50,2401
Polymers50,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucoidan lyase FdlA


Theoretical massNumber of molelcules
Total (without water)50,2401
Polymers50,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.068, 58.150, 88.164
Angle α, β, γ (deg.)90.161, 101.691, 92.115
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A' and (resid 1 through 31 or resid 33...
211(chain 'B' and (resid 1 through 31 or resid 33...

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Components

#1: Protein Fucoidan lyase FdlA


Mass: 50240.434 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: Y242F
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.: 582 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
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: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→86 Å / Num. obs: 57344 / % possible obs: 91 % / Redundancy: 1.7 % / Biso Wilson estimate: 15.35 Å2 / Rrim(I) all: 0.17 / Net I/σ(I): 3.9
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 1.7 % / Num. unique obs: 8676 / Rrim(I) all: 0.336

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XZF

7xzf


Resolution: 2.08→27.75 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2801 4.89 %
Rwork0.173 54475 -
obs0.1757 57276 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.33 Å2
Refinement stepCycle: LAST / Resolution: 2.08→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 0 582 7320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786993
X-RAY DIFFRACTIONf_angle_d0.95459534
X-RAY DIFFRACTIONf_chiral_restr0.06641074
X-RAY DIFFRACTIONf_plane_restr0.00561278
X-RAY DIFFRACTIONf_dihedral_angle_d17.27822524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.120.22751410.1712785X-RAY DIFFRACTION94.51
2.12-2.160.23861420.16552880X-RAY DIFFRACTION94.7
2.16-2.20.251340.16852811X-RAY DIFFRACTION94.3
2.2-2.240.2612840.18411586X-RAY DIFFRACTION82.1
2.24-2.290.259760.19421438X-RAY DIFFRACTION91.1
2.29-2.340.26111600.16862846X-RAY DIFFRACTION94.62
2.34-2.40.24641630.16842813X-RAY DIFFRACTION94.87
2.4-2.470.24521560.17232847X-RAY DIFFRACTION95.09
2.47-2.540.23291530.18192815X-RAY DIFFRACTION94.22
2.54-2.620.26691250.18562877X-RAY DIFFRACTION96.25
2.62-2.710.2711320.20172859X-RAY DIFFRACTION93.82
2.71-2.820.23531480.17252859X-RAY DIFFRACTION96.44
2.82-2.950.26931350.17822914X-RAY DIFFRACTION96.03
2.95-3.110.20881560.17972907X-RAY DIFFRACTION96.93
3.11-3.30.24931270.17752861X-RAY DIFFRACTION95.65
3.3-3.560.23761860.18392820X-RAY DIFFRACTION95.07
3.56-3.910.23461540.18292881X-RAY DIFFRACTION95.8
3.91-4.480.16571300.14492891X-RAY DIFFRACTION95.6
4.48-5.630.16891420.14682897X-RAY DIFFRACTION97.09
5.63-27.750.18431570.17612888X-RAY DIFFRACTION96.48
Refinement TLS params.Method: refined / Origin x: 58.6755536894 Å / Origin y: -31.2263693784 Å / Origin z: -67.5085148902 Å
111213212223313233
T0.0411233788185 Å2-0.000488448500195 Å2-0.002162298102 Å2-0.0443695432599 Å20.00259061512457 Å2--0.0457464538307 Å2
L0.0201727055994 °2-0.0233183655252 °2-0.0277045265779 °2-0.0388131017785 °20.0423902674041 °2--0.102474610751 °2
S-0.00637419966721 Å °-0.000419879573106 Å °0.00507875729565 Å °-0.00283877212926 Å °-0.00507663041817 Å °0.00897396313523 Å °-0.00631535678341 Å °0.00467451018045 Å °1.48365757625E-11 Å °
Refinement TLS groupSelection details: all

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