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- PDB-4q8k: Crystal structure of polysaccharide lyase family 18 aly-SJ02 P-CATD -

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Basic information

Entry
Database: PDB / ID: 4q8k
TitleCrystal structure of polysaccharide lyase family 18 aly-SJ02 P-CATD
ComponentsAlginase
KeywordsLYASE / Alginate Lyase
Function / homology
Function and homology information


Alginate lyase 2 / Alginate lyase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.646 Å
AuthorsDong, S. / Li, C.Y. / Zhang, Y.Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Molecular insight into the role of the N-terminal extension in the maturation, substrate recognition, and catalysis of a bacterial alginate lyase from polysaccharide lyase family 18.
Authors: Dong, S. / Wei, T.D. / Chen, X.L. / Li, C.Y. / Wang, P. / Xie, B.B. / Qin, Q.L. / Zhang, X.Y. / Pang, X.H. / Zhou, B.C. / Zhang, Y.Z.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1314
Polymers40,8991
Non-polymers2323
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.361, 46.361, 386.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-873-

HOH

21A-907-

HOH

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Components

#1: Protein Alginase


Mass: 40899.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas (bacteria) / Strain: SM0524 / Production host: Escherichia coli (E. coli) / References: UniProt: B2LME8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM MES (pH 7.5), 25% (w/v) PEG 4000, 150mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.646→50 Å / Num. all: 29301 / Num. obs: 29301 / % possible obs: 91.9 %
Reflection shellResolution: 1.65→1.71 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.646→35.635 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1470 5.03 %RANDOM
Rwork0.2029 ---
obs0.2041 29196 92.06 %-
all-29301 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.948 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9833 Å2-0 Å2-0 Å2
2--4.9833 Å20 Å2
3----9.9666 Å2
Refinement stepCycle: LAST / Resolution: 1.646→35.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 11 329 2097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011801
X-RAY DIFFRACTIONf_angle_d1.1182445
X-RAY DIFFRACTIONf_dihedral_angle_d14.753641
X-RAY DIFFRACTIONf_chiral_restr0.075271
X-RAY DIFFRACTIONf_plane_restr0.005325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6462-1.70510.23691470.2569282997
1.7051-1.77330.27461560.2332284498
1.7733-1.85410.2681550.2387289998
1.8541-1.95180.27551340.2463265091
1.9518-2.07410.26711690.193288099
2.0741-2.23420.22371450.2023269090
2.2342-2.4590.22831280.2006246082
2.459-2.81470.21951650.1968299199
2.8147-3.54570.22171570.1948306398
3.5457-35.6430.20561140.1942242071
Refinement TLS params.Method: refined / Origin x: -14.4431 Å / Origin y: 13.52 Å / Origin z: -14.2791 Å
111213212223313233
T0.0956 Å20.0272 Å20.0022 Å2-0.2886 Å2-0.0259 Å2--0.1998 Å2
L0.6998 °20.0544 °20.0416 °2-0.6496 °20.2558 °2--1.5205 °2
S-0.0022 Å °-0.1653 Å °0.027 Å °-0.0224 Å °0.0013 Å °-0.0128 Å °-0.0156 Å °0.0735 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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