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- PDB-6tn6: X-ray structure of the endo-beta-1,4-mannanase from Thermotoga pe... -

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Basic information

Entry
Database: PDB / ID: 6tn6
TitleX-ray structure of the endo-beta-1,4-mannanase from Thermotoga petrophila
ComponentsMannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
KeywordsHYDROLASE / Mannanase / hyperthermophile
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Carbohydrate binding module 27 / Carbohydrate binding module 27 / Mannan endo-1,4-beta-mannosidase-like / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / CARBONATE ION / DI(HYDROXYETHYL)ETHER / Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
Similarity search - Component
Biological speciesThermotoga petrophila RKU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
Authorsda Silva, V.M. / Squina, F.M. / Sperenca, M. / Martin, L. / Muniz, J.R.C. / Garcia, W. / Nicolet, Y.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: High-resolution structure of a modular hyperthermostable endo-beta-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain.
Authors: da Silva, V.M. / Cabral, A.D. / Speranca, M.A. / Squina, F.M. / Muniz, J.R.C. / Martin, L. / Nicolet, Y. / Garcia, W.
History
DepositionDec 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,30221
Polymers73,8311
Non-polymers1,47120
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-10 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.710, 174.710, 174.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1475-

HOH

21A-1498-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5


Mass: 73830.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila RKU-1 (bacteria) / Gene: Tpet_1542 / Production host: Escherichia coli (E. coli)
References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase

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Non-polymers , 10 types, 522 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen D12 condition

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→46.693 Å / Num. obs: 303865 / % possible obs: 99.9 % / Redundancy: 6.67 % / CC1/2: 1 / Rrim(I) all: 0.043 / Rsym value: 0.042 / Net I/σ(I): 23.26
Reflection shellResolution: 1.45→1.49 Å / Num. unique obs: 11434 / CC1/2: 0.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXv1.15.2-3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZ9

3pz9


Resolution: 1.45→46.693 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 17.81
RfactorNum. reflection% reflection
Rfree0.1506 15209 5.01 %
Rwork0.1374 --
obs0.1381 155320 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.37 Å2 / Biso mean: 33.456 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 1.45→46.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 208 504 4485
Biso mean--71.31 45.32 -
Num. residues----465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4501-1.46660.31925020.3486940897
1.4666-1.48380.33975030.3268968199
1.4838-1.50190.31995070.3119957699
1.5019-1.52090.30545000.306952899
1.5209-1.54090.32665070.31389678100
1.5409-1.56210.29235140.2869734100
1.5621-1.58440.27325070.27659604100
1.5844-1.6080.29155120.25549709100
1.608-1.63320.25415070.2429629100
1.6332-1.65990.21785130.22649628100
1.6599-1.68860.24255060.212963399
1.6886-1.71930.22145060.20469592100
1.7193-1.75230.20475120.1891966899
1.7523-1.78810.19374970.1774956399
1.7881-1.8270.18315040.17329611100
1.827-1.86950.18875180.16549756100
1.8695-1.91620.17015020.15689624100
1.9162-1.9680.16255090.14619603100
1.968-2.0260.16475060.14019694100
2.026-2.09130.1585150.12719611100
2.0913-2.16610.15195110.1244962099
2.1661-2.25280.12295020.11499564100
2.2528-2.35530.12965030.11619696100
2.3553-2.47950.12845120.11019666100
2.4795-2.63490.11695050.10439635100
2.6349-2.83830.12425100.11269691100
2.8383-3.12380.13395040.1173957699
3.1238-3.57570.12135040.1129951098
3.5757-4.50450.10825050.10079640100
4.5045-46.6930.15575060.1407952898
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)
11.7109-0.5587-0.89312.1167-0.13793.06420.07420.12060.0841-0.0383-0.05370.0379-0.0311-0.1194-0.03860.13830.00070.01950.1638-0.01220.185547.363585.8096105.2065
20.6585-0.2739-0.22260.67780.16680.3369-0.01340.00340.00050.0537-0.02020.00370.019-0.00160.03410.2077-0.00060.02260.198-0.02170.190150.6874.9822108.1497
34.14590.76970.79282.73660.51872.9019-0.0319-0.16260.20960.0796-0.0106-0.382-0.11090.34050.02820.23230.02760.05020.2325-0.02110.3382.733471.430993.3678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 84 )A30 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 408 )A85 - 408
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 494 )A409 - 494

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