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- PDB-7w18: Complex structure of alginate lyase PyAly with M5 -

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Basic information

Entry
Database: PDB / ID: 7w18
TitleComplex structure of alginate lyase PyAly with M5
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: 1.7 Å
AuthorsLiu, W.Z. / Lyu, Q.Q. / 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)27,8622
Polymers26,9631
Non-polymers8991
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint14 kcal/mol
Surface area9420 Å2
Unit cell
Length a, b, c (Å)62.272, 62.272, 113.271
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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Components

#1: Protein Alginate lyase


Mass: 26963.125 Da / Num. of mol.: 1 / Mutation: H125A, Y223A
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- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 898.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122A-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][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.: 136 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: HEPES sodium, propanol, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28715 / % possible obs: 100 % / Redundancy: 18.3 % / Rpim(I) all: 0.031 / Net I/σ(I): 21.1
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1283 / Rpim(I) all: 0.386

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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: 1.7→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.295 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 1327 5.1 %RANDOM
Rwork0.2435 ---
obs0.2457 24767 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.46 Å2 / Biso mean: 15.127 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 61 136 1857
Biso mean--17.27 23.81 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191770
X-RAY DIFFRACTIONr_angle_refined_deg2.791.9852405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9855212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.51221.42977
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59615280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0581521
X-RAY DIFFRACTIONr_chiral_restr0.2250.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211328
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 59 -
Rwork0.297 1169 -
all-1228 -
obs--59.32 %

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