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- PDB-8d89: Crystal structure of a novel GH5 enzyme retrieved from capybara g... -

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Basic information

Entry
Database: PDB / ID: 8d89
TitleCrystal structure of a novel GH5 enzyme retrieved from capybara gut metagenome
ComponentsGlycoside Hydrolase Family 5 Endo-mannanase
KeywordsHYDROLASE / CAZyme / TIM-barrel
Function / homologyChem-1PG / ACETATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsMartins, M.P. / Morais, M.A.B. / Murakami, M.T.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)306135/2016-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)142332/2017-8 Brazil
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-beta-mannans.
Authors: Martins, M.P. / Morais, M.A.B. / Persinoti, G.F. / Galinari, R.H. / Yu, L. / Yoshimi, Y. / Passos Nunes, F.B. / Lima, T.B. / Barbieri, S.F. / Silveira, J.L.M. / Lombard, V. / Terrapon, N. / ...Authors: Martins, M.P. / Morais, M.A.B. / Persinoti, G.F. / Galinari, R.H. / Yu, L. / Yoshimi, Y. / Passos Nunes, F.B. / Lima, T.B. / Barbieri, S.F. / Silveira, J.L.M. / Lombard, V. / Terrapon, N. / Dupree, P. / Henrissat, B. / Murakami, M.T.
History
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside Hydrolase Family 5 Endo-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1455
Polymers45,7751
Non-polymers3704
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.600, 58.860, 60.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycoside Hydrolase Family 5 Endo-mannanase / GH5 Endo-mannanase


Mass: 45775.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 19% (w/v) PEG 600, 0.1 M sodium acetate pH 5.0, and 0.2 M of magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.45864 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45864 Å / Relative weight: 1
ReflectionResolution: 1.6→42.765 Å / Num. obs: 54691 / % possible obs: 94.67 % / Redundancy: 12.61 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.12
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 5045 / CC1/2: 0.51

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.765 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 2735 5 %
Rwork0.1708 51956 -
obs0.172 54691 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.02 Å2 / Biso mean: 23.3586 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 1.6→42.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 23 415 3487
Biso mean--38.83 31.89 -
Num. residues----382
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.62760.37251250.3418236588
1.6276-1.65720.31351270.2954242990
1.6572-1.68910.2681300.2636246991
1.6891-1.72360.27261300.2503247492
1.7236-1.7610.31151310.2285248992
1.761-1.8020.24861330.2136252393
1.802-1.84710.21481340.1986254793
1.8471-1.8970.23551340.1875254394
1.897-1.95280.20691350.1872256694
1.9528-2.01590.2221370.1764259195
2.0159-2.08790.21231340.1609256395
2.0879-2.17150.20221380.1585262295
2.1715-2.27030.1871380.1529261096
2.2703-2.390.16971380.1569263197
2.39-2.53980.21791410.1623266896
2.5398-2.73580.18261420.1655269398
2.7358-3.01110.18391420.1674270598
3.0111-3.44660.18891430.1593272998
3.4466-4.34170.16351480.1412279699
4.3417-42.7650.15141550.1612943100
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)
12.19-0.554-0.73891.70390.44391.46-0.03490.14640.0449-0.04580.0587-0.1666-0.05070.1546-0.04090.1577-0.0258-0.02250.155-0.01370.120329.468919.130115.2716
24.8852-0.092.20321.6407-0.34821.7719-0.06750.0330.1928-0.0108-0.0060.1574-0.1594-0.08840.07960.13140.02450.02230.1196-0.02550.097614.52723.527813.5102
32.61741.84272.05362.10311.29572.28380.02960.09420.10850.0101-0.02260.21540.0183-0.0818-0.01270.13140.0269-0.01480.1002-0.01010.14219.83711.3096.4034
46.40874.35893.02434.57012.05341.841-0.11830.13190.2699-0.19330.05190.2159-0.184-0.00170.07530.14680.02510.01590.17060.01050.095216.90418.43613.1194
52.14532.32182.14156.32632.07862.15290.1329-0.1182-0.11210.1684-0.15090.38580.1302-0.24140.01290.0982-0.00630.00860.1874-0.01750.18769.526-1.18819.723
67.39375.6299-1.68817.6485-1.59221.503-0.19530.31710.0409-0.56270.18250.16540.05950.0515-0.02050.14940.0155-0.02340.136-0.00470.078117.90438.065-0.9064
71.3421.9344-0.83766.7086-2.08451.56710.00230.073-0.0502-0.0654-0.01460.10430.084-0.01470.0110.10730.02-0.02580.1299-0.01260.087219.6994-2.47018.4043
82.3684-0.61441.19284.0173-0.36462.71170.05790.0981-0.0779-0.1345-0.0447-0.22750.04570.1189-0.01380.07920.0070.0180.1246-0.01010.111424.1686-1.77157.4409
91.1533-0.14170.09151.9951.42742.86420.0335-0.0937-0.18820.12960.0140.02230.1043-0.0897-0.04450.12270.0053-0.02150.1303-0.00160.131125.7475-2.239119.8463
103.32-1.1791-1.05942.27190.70761.59190.0304-0.0706-0.09570.1353-0.05620.064-0.0569-0.01250.01530.1154-0.022-0.0310.08060.00950.071324.59979.258827.1891
118.2132-2.9834-5.47464.08284.08478.67130.0954-0.1404-0.00340.0470.1104-0.3094-0.22360.5289-0.22470.169-0.0144-0.04680.14390.01190.124232.925812.311628.8673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 107 )A32 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 149 )A108 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 180 )A150 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 207 )A181 - 207
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 225 )A208 - 225
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 243 )A226 - 243
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 274 )A244 - 274
8X-RAY DIFFRACTION8chain 'A' and (resid 275 through 297 )A275 - 297
9X-RAY DIFFRACTION9chain 'A' and (resid 298 through 344 )A298 - 344
10X-RAY DIFFRACTION10chain 'A' and (resid 345 through 382 )A345 - 382
11X-RAY DIFFRACTION11chain 'A' and (resid 383 through 404 )A383 - 404

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