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- PDB-7w12: Complex structure of alginate lyase AlyB-OU02 with G9 -

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Basic information

Entry
Database: PDB / ID: 7w12
TitleComplex structure of alginate lyase AlyB-OU02 with G9
ComponentsAlginate lyase
KeywordsLYASE / PL7 family / alginate lyase / complex
Function / homology
Function and homology information


Alginate lyase 2 / Alginate lyase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Alginate lyase 2 / Alginate lyase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio splendidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)55,8184
Polymers54,0221
Non-polymers1,7953
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint4 kcal/mol
Surface area20310 Å2
Unit cell
Length a, b, c (Å)156.627, 156.627, 60.784
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312

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Components

#1: Protein Alginate lyase


Mass: 54022.445 Da / Num. of mol.: 1 / Mutation: H388A, Y466A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio splendidus (bacteria) / Gene: BTO12_02585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S7V314
#2: Polysaccharide alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid- ...alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 1603.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-4LGulpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a1121A-1a_1-5]/1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{}}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.02 Å3/Da / Density % sol: 69.41 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: Li2SO4, Tris-HCl pH 8.0, PEG 4000

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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: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 40570 / % possible obs: 100 % / Redundancy: 14.6 % / CC1/2: 0.998 / Net I/σ(I): 45
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 2005 / CC1/2: 0.917

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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
Starting model: 5ZU5

5zu5


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.044 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 2017 5 %RANDOM
Rwork0.194 ---
obs0.1961 38264 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.63 Å2 / Biso mean: 32.6 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 119 132 4003
Biso mean--38.58 28.39 -
Num. residues----490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193964
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9755403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3245491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.725.08187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66215610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2761520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213029
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 137 -
Rwork0.238 2813 -
all-2950 -
obs--99.97 %

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