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- PDB-6yq4: Crystal structure of Fusobacterium nucleatum tannase -

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Basic information

Entry
Database: PDB / ID: 6yq4
TitleCrystal structure of Fusobacterium nucleatum tannase
ComponentsTannase
KeywordsHYDROLASE / Tannase / Colorectal Cancer / Pathogen / Gallotannins
Function / homologyAlpha/Beta hydrolase fold / SPERMIDINE / Uncharacterized protein
Function and homology information
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsMancheno, J.M. / Anguita, J. / Rodriguez, H.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2015-65327 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-096494-B-100 Spain
CitationJournal: Microb Biotechnol / Year: 2022
Title: A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance.
Authors: Mancheno, J.M. / Atondo, E. / Tomas-Cortazar, J. / Luis Lavin, J. / Plaza-Vinuesa, L. / Martin-Ruiz, I. / Barriales, D. / Palacios, A. / Daniel Navo, C. / Sampedro, L. / Pena-Cearra, A. / ...Authors: Mancheno, J.M. / Atondo, E. / Tomas-Cortazar, J. / Luis Lavin, J. / Plaza-Vinuesa, L. / Martin-Ruiz, I. / Barriales, D. / Palacios, A. / Daniel Navo, C. / Sampedro, L. / Pena-Cearra, A. / Angel Pascual-Itoiz, M. / Castelo, J. / Carreras-Gonzalez, A. / Castellana, D. / Pellon, A. / Delgado, S. / Ruas-Madiedo, P. / de Las Rivas, B. / Abecia, L. / Munoz, R. / Jimenez-Oses, G. / Anguita, J. / Rodriguez, H.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tannase
B: Tannase
C: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,04910
Polymers165,5553
Non-polymers4947
Water7,332407
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3013
Polymers55,1851
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4474
Polymers55,1851
Non-polymers2623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3013
Polymers55,1851
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.840, 91.067, 124.068
Angle α, β, γ (deg.)90.000, 101.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tannase /


Mass: 55184.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: FN0616 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RFS1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→47.791 Å / Num. obs: 60896 / % possible obs: 99 % / Redundancy: 6.62 % / CC1/2: 0.997 / Net I/σ(I): 15.31
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 6014 / CC1/2: 0.923 / % possible all: 98.74

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J0D

4j0d


Resolution: 2.399→47.79 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28
RfactorNum. reflection% reflection
Rfree0.2509 3103 5.1 %
Rwork0.1711 --
obs0.1752 60840 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.11 Å2 / Biso mean: 45.6597 Å2 / Biso min: 13.68 Å2
Refinement stepCycle: final / Resolution: 2.399→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11248 0 31 407 11686
Biso mean--42.8 39.23 -
Num. residues----1436
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.399-2.4360.36541310.2528254997
2.436-2.47590.33131570.2496264699
2.4759-2.51860.33891400.2394256999
2.5186-2.56440.3161330.2277263299
2.5644-2.61380.31441200.2117257998
2.6138-2.66710.31761380.2221261299
2.6671-2.72510.28541350.2132632100
2.7251-2.78850.30091380.211264899
2.7885-2.85820.28011540.2187259299
2.8582-2.93550.31161440.20832645100
2.9355-3.02180.30021340.192262699
3.0218-3.11930.27861320.1907265199
3.1193-3.23080.29971710.1926255999
3.2308-3.36010.26691380.1751260498
3.3601-3.5130.25591420.1656262199
3.513-3.69820.22951560.15542636100
3.6982-3.92980.26021310.15282657100
3.9298-4.2330.2061500.1391262899
4.233-4.65870.18131280.1196266199
4.6587-5.3320.19031610.1322259198
5.332-6.71480.2091420.1599266899
6.7148-47.790.20931280.1513273199
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)
12.69842.6911-0.63767.321-3.34943.37180.1123-0.2190.47770.2226-0.17090.2732-0.461-0.03340.03950.49720.0445-0.05440.2548-0.13740.3757-17.6563.1061-1.5523
21.63440.0330.30151.99260.35871.23790.0446-0.21520.2294-0.0001-0.14170.1011-0.1636-0.16260.07680.280.0211-0.01550.221-0.03710.1899-17.6159-13.3387-6.0048
33.5122-2.44611.43081.8726-0.5163.49190.09510.1069-0.09740.18280.0497-0.29190.05250.2286-0.2030.2627-0.01250.01950.21190.07250.1925-6.3642-34.2624-6.6488
41.5324-0.23850.15192.03150.38241.360.07660.0244-0.1163-0.1223-0.1271-0.05410.09810.03430.0750.26080.02-0.01610.18090.01680.1834-12.2732-28.4455-14.5839
52.168-1.8575-1.45028.02172.67375.2905-0.195-0.1791-0.00770.24080.0759-0.50950.88071.21440.06090.49210.24520.01560.79920.05830.2865-10.0147-37.4642-51.6785
61.1681-0.4327-0.86752.39560.03033.209-0.09480.15110.0581-0.19810.0334-0.21650.33030.50470.01610.33430.04190.03240.38540.03650.1793-21.3713-30.5472-52.3722
74.61860.3898-0.72441.92870.53125.17370.0398-0.2301-0.35430.12890.10030.33820.5253-0.7848-0.09970.41290.00450.04010.3744-0.02340.2086-45.0712-28.4093-37.3237
81.26970.1333-0.17771.47690.18233.159-0.03550.16830.0203-0.09760.00530.22640.3348-0.76850.05510.3762-0.0404-0.01960.44490.04250.223-43.3016-28.7582-48.5036
95.164-0.8245-0.32683.20480.98982.9049-0.17540.312-0.389-0.38020.2444-0.57920.18640.4272-0.11660.58210.11840.08690.4272-0.08650.329323.1766-84.6652-42.804
105.5831-1.5685-2.17112.95191.45371.3204-0.1499-0.240.6784-0.2110.2697-0.54040.11860.1961-0.13860.41140.09270.07420.3515-0.0060.306121.6072-72.8803-42.8642
111.8153-0.5765-0.32162.38710.6751.616-0.08740.26690.019-0.30530.01460.17120.1439-0.10810.06860.33520.0197-0.03970.3190.01090.16973.8071-70.3335-36.8928
122.2025-0.8068-0.09961.92560.33911.3832-0.14520.00940.23740.00230.1170.01260.0734-0.01030.03380.30170.0469-0.0460.25060.00310.21444.8842-60.9138-29.2238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 58 )A5 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 239 )A59 - 239
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 279 )A240 - 279
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 494 )A280 - 494
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 58 )B5 - 58
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 211 )B59 - 211
7X-RAY DIFFRACTION7chain 'B' and (resid 212 through 279 )B212 - 279
8X-RAY DIFFRACTION8chain 'B' and (resid 280 through 494 )B280 - 494
9X-RAY DIFFRACTION9chain 'C' and (resid 5 through 81 )C5 - 81
10X-RAY DIFFRACTION10chain 'C' and (resid 82 through 114 )C82 - 114
11X-RAY DIFFRACTION11chain 'C' and (resid 115 through 279 )C115 - 279
12X-RAY DIFFRACTION12chain 'C' and (resid 280 through 494 )C280 - 494

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