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- PDB-7w16: Complex structure of alginate lyase AlyV with M8 -

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Basic information

Entry
Database: PDB / ID: 7w16
TitleComplex structure of alginate lyase AlyV with M8
Componentsalginate lyase
KeywordsLYASE / PL7 family / alginate lyase / complex
Biological speciesVibrio pelagius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)33,9053
Polymers33,4421
Non-polymers4622
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint10 kcal/mol
Surface area11780 Å2
Unit cell
Length a, b, c (Å)80.405, 80.405, 113.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

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Components

#1: Protein alginate lyase


Mass: 33442.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio pelagius (bacteria) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122A-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.17 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate tribasic dihydrate

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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: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 34336 / % possible obs: 100 % / Redundancy: 17.8 % / Rpim(I) all: 0.049 / Net I/σ(I): 20.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3385 / Rpim(I) all: 0.281

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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: 1.9→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.241 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 1706 5.1 %RANDOM
Rwork0.1425 ---
obs0.145 32045 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.85 Å2 / Biso mean: 22.158 Å2 / Biso min: 4.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 31 123 2215
Biso mean--28.73 30.31 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192159
X-RAY DIFFRACTIONr_angle_refined_deg2.3071.962932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3215267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81225.347101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67815346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.681155
X-RAY DIFFRACTIONr_chiral_restr0.1840.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211665
X-RAY DIFFRACTIONr_rigid_bond_restr7.19632159
X-RAY DIFFRACTIONr_sphericity_free22.471534
X-RAY DIFFRACTIONr_sphericity_bonded18.45852195
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 134 -
Rwork0.183 2005 -
all-2139 -
obs--86.92 %

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