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- PDB-5yj6: The exoglucanase CelS from Clostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 5yj6
TitleThe exoglucanase CelS from Clostridium thermocellum
ComponentsDockerin type I repeat-containing protein
KeywordsHYDROLASE / activity / cellulosome / exocellulase / substrate specificity
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process
Similarity search - Function
Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex ...Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-33O / : / Glycosyl hydrolase family 48 protein CelS
Similarity search - Component
Biological speciesRuminiclostridium thermocellum DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsLiu, Y.J. / Liu, S.Y. / Dong, S. / Li, R.M. / Feng, Y.G. / Cui, Q.
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum
Authors: Liu, Y.J. / Liu, S. / Dong, S. / Li, R. / Feng, Y. / Cui, Q.
History
DepositionOct 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: 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

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Assembly

Deposited unit
A: Dockerin type I repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9382
Polymers74,3471
Non-polymers5911
Water14,862825
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21990 Å2
Unit cell
Length a, b, c (Å)96.003, 101.065, 58.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1479-

HOH

21A-1552-

HOH

31A-1593-

HOH

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Components

#1: Protein Dockerin type I repeat-containing protein


Mass: 74347.039 Da / Num. of mol.: 1 / Fragment: UNP residues 31-666
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum DSM 1313 (bacteria)
Gene: SAMN04515622_0728 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A286AKY4, UniProt: C7ED31*PLUS
#2: Chemical ChemComp-33O / 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol / Tridecaethyleneglycol


Mass: 590.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H54O14
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 1.77 Å3/Da / Density % sol: 36.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 200mM sodium formate, 20% PEG3350

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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: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.43→101.07 Å / Num. obs: 100821 / % possible obs: 94.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 16 / Num. measured all: 737296 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.476.80.8583632853530.8390.3470.9272.369.2
6.4-101.076.60.023859313100.9990.010.0254997.6

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Processing

Software
NameVersionClassification
REFMAC(phenix.refine: 1.8.4_1496)refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L2A

1l2a


Resolution: 1.43→38.373 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 1981 1.97 %
Rwork0.1518 --
obs0.1523 100746 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.97 Å2 / Biso mean: 23.3299 Å2 / Biso min: 11.05 Å2
Refinement stepCycle: final / Resolution: 1.43→38.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 40 825 5973
Biso mean--48.19 33.67 -
Num. residues----636
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)
10.9619-0.67060.13073.32190.42230.94110.05720.165-0.0479-0.1777-0.06160.03320.0399-0.0513-0.00460.13020.0056-0.01460.1675-0.00920.0778-23.09212.6838-25.9249
21.8163-0.5076-0.07271.1028-0.16870.3448-0.00830.06940.2640.026-0.0475-0.3625-0.07340.07420.04740.1399-0.0077-0.02080.12790.0510.2287-8.593135.2163-16.2223
30.8079-0.1234-0.05830.7591-0.11910.4249-0.0257-0.0249-0.02630.0712-0.0264-0.1072-0.01830.00860.04870.09980.0045-0.02870.10030.01340.1489-12.992913.1057-5.2105
41.0856-0.50490.04632.5519-0.25570.14170.02350.10870.05740.0922-0.01150.2757-0.0363-0.0559-0.00810.13620.00820.01060.15570.01140.0672-31.762727.6926-17.8437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 119 )A28 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 253 )A120 - 253
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 564 )A254 - 564
4X-RAY DIFFRACTION4chain 'A' and (resid 565 through 663 )A565 - 663

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