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- PDB-7w13: Complex structure of alginate lyase PyAly with M8 -

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Basic information

Entry
Database: PDB / ID: 7w13
TitleComplex structure of alginate lyase PyAly with M8
ComponentsAlginate lyase
KeywordsLYASE / PL7 family / alginate lyase / complex
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase
Function and homology information
Biological speciesNeopyropia yezoensis (susabi-nori)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, W.Z. / Lyu, Q.Q. / Li, Z.J. / Zhang, K.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2022
Title: Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements.
Authors: Zhang, K. / Li, Z. / Zhu, Q. / Cao, H. / He, X. / Zhang, X.H. / Liu, W. / Lyu, Q.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6022
Polymers27,0551
Non-polymers5461
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint4 kcal/mol
Surface area9600 Å2
Unit cell
Length a, b, c (Å)47.313, 64.523, 73.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alginate lyase


Mass: 27055.221 Da / Num. of mol.: 1 / Mutation: H125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neopyropia yezoensis (susabi-nori) / Gene: PyAly / Production host: Escherichia coli (E. coli) / References: UniProt: D2KX85
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122A-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: Imidazole, Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 29611 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rsym value: 0.077 / Net I/σ(I): 30.4
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 1467 / Rsym value: 0.077 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→39.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 1.899 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1398 5 %RANDOM
Rwork0.2094 ---
obs0.2109 26425 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.09 Å2 / Biso mean: 14.153 Å2 / Biso min: 6.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.65→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 37 89 1795
Biso mean--20.67 18.42 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191745
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.972364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.38621.55877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96115287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.071522
X-RAY DIFFRACTIONr_chiral_restr0.1540.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211311
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 108 -
Rwork0.224 1924 -
all-2032 -
obs--99.27 %

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