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- PDB-5zqi: Alginate lyase AlgAT5 from Polysaccharide Lyase family 7 -

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Basic information

Entry
Database: PDB / ID: 5zqi
TitleAlginate lyase AlgAT5 from Polysaccharide Lyase family 7
ComponentsAlginate lyase AlgAT5
KeywordsLYASE / Alginate lyase / PL7 / b-sandwich fold
Function / homologyLyases; Carbon-oxygen lyases; Acting on polysaccharides / Alginate lyase 2 / Alginate lyase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / Alginate lyase AlgAT5
Function and homology information
Biological speciesDefluviitalea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSu, H. / Dong, S. / Feng, Y.G. / Ji, S.Q. / Lu, M. / Li, F.L.
Citation
Journal: To Be Published
Title: Alginate lyase AlgAT5 from Polysaccharide Lyase family 7
Authors: Su, H. / Dong, S. / Feng, Y.G. / Ji, S.Q. / Lu, M. / Li, F.L.
#1: Journal: Appl. Environ. Microbiol. / Year: 2016
Title: Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae.
Authors: Ji, S.Q. / Wang, B. / Lu, M. / Li, F.L.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase AlgAT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0412
Polymers30,9451
Non-polymers961
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.020, 76.380, 83.910
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 AlgAT5


Mass: 30944.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Defluviitalea (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A4V8GZK9*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.2M potassium nitrate, 20% PEG3350, pH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→41.95 Å / Num. obs: 40624 / % possible obs: 97 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.85 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.085 / Rrim(I) all: 0.201 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.535.50.31620160.8720.1490.3598.6
8.22-41.953.40.27870.8070.1390.30523.9

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX1.13-2998_1496refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAI

1uai


Resolution: 1.5→20.228 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.51
RfactorNum. reflection% reflection
Rfree0.1878 2000 4.93 %
Rwork0.1671 --
obs0.1682 40560 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.29 Å2 / Biso mean: 16.7292 Å2 / Biso min: 5.12 Å2
Refinement stepCycle: final / Resolution: 1.5→20.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 5 573 2267
Biso mean--32.99 33.11 -
Num. residues----216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53750.20491440.16572772291699
1.5375-1.57910.16971430.15242764290799
1.5791-1.62550.17421450.1492795294099
1.6255-1.67790.16541450.14252779292499
1.6779-1.73790.18031450.14762818296399
1.7379-1.80740.17461450.157627852930100
1.8074-1.88960.19151460.15612812295899
1.8896-1.98920.2251460.2022818296499
1.9892-2.11370.19071470.154528382985100
2.1137-2.27670.22251470.183328292976100
2.2767-2.50540.16651480.152828492997100
2.5054-2.86710.1591490.155728813030100
2.8671-3.60890.18151430.15862769291295
3.6089-20.23020.20591070.21432051215867
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0462-0.46160.07233.3136-0.52922.49060.0553-0.1630.07450.15390.02120.0511-0.1004-0.0487-0.05760.0796-0.010.03030.0662-0.00810.048110.821441.13432.3617
21.5648-0.0069-0.64163.455-0.22712.39060.0807-0.0607-0.14430.072-0.0492-0.03420.0894-0-0.03490.04490.0083-0.010.05160.00530.056616.953633.504929.8528
31.4536-0.34780.48661.3734-0.43191.42950.03010.0864-0.09850.00670.02540.06250.01710.0081-0.04810.0452-0.00890.00580.0519-0.01430.070413.803936.654117.8075
41.7545-0.5791-1.31146.2961-1.50274.98890.02220.2289-0.2202-0.33380.0343-0.02950.26010.2478-0.05480.09280.03680.00040.111-0.04290.130624.001129.948610.4667
51.24360.01410.47120.769-0.30611.7371-0.01450.1598-0.0594-0.07170.0201-0.0740.00450.1837-0.00760.0591-0.00370.00820.0794-0.0260.072620.081239.154111.3517
61.1809-0.79140.72544.6308-0.97321.42960.03-0.0261-0.11260.19090.0215-0.13230.05780.0411-0.04340.05950.0090.02410.0648-0.01630.051419.326632.799425.054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 66 )A29 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 93 )A67 - 93
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 153 )A94 - 153
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 170 )A154 - 170
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 216 )A171 - 216
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 243 )A217 - 243

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