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- PDB-6r3u: Endo-levanase BT1760 mutant E221A from Bacteroides thetaiotaomicr... -

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Basic information

Entry
Database: PDB / ID: 6r3u
TitleEndo-levanase BT1760 mutant E221A from Bacteroides thetaiotaomicron complexed with levantetraose
ComponentsGlycoside hydrolase family 32
KeywordsHYDROLASE / glycoside hydrolase 32 / 5-fold beta-propeller / beta-sandwich / substrate complex
Function / homology
Function and homology information


beta-fructofuranosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
GH32, BT1760-like, C-terminal domain / GH32, BT1760-like, C-terminal domain / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-fructofuranosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEek, P. / Ernits, K. / Lukk, T. / Alamae, T.
Funding support Estonia, 2items
OrganizationGrant numberCountry
Estonian Research CouncilPUT1050 Estonia
Estonian Research CouncilIUT19-9 Estonia
CitationJournal: Sci Rep / Year: 2019
Title: First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron.
Authors: Ernits, K. / Eek, P. / Lukk, T. / Visnapuu, T. / Alamae, T.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9347
Polymers57,8601
Non-polymers1,0746
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-29 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.114, 112.334, 174.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Glycoside hydrolase family 32 /


Mass: 57860.004 Da / Num. of mol.: 1 / Mutation: E221A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1760 / Plasmid: pURI3-Cter / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6W6
#2: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-6DFrufb2-6DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[ha122h-2b_2-5]/1-1-1-1/a6-b2_b6-c2_c6-d2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3.34 Å3/Da / Density % sol: 63.2 % / Description: rod clusters
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16 mg/ml protein; 12-14% (w/v) PEG 6000, 0.5 mM ZnCl2, 0.1 M MES-NaOH, pH 6.5; 2:1 ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→47.21 Å / Num. obs: 60697 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 30.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.129 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5956 / CC1/2: 0.74 / Rpim(I) all: 0.424 / Rrim(I) all: 1.208 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.15rc3_3435refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R3R

6r3r


Resolution: 1.9→47.21 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / Phase error: 19.2158
RfactorNum. reflection% reflection
Rfree0.19 1438 2.37 %
Rwork0.161 --
obs-60564 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 65 326 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174199
X-RAY DIFFRACTIONf_angle_d1.03345705
X-RAY DIFFRACTIONf_chiral_restr0.0661586
X-RAY DIFFRACTIONf_plane_restr0.0075737
X-RAY DIFFRACTIONf_dihedral_angle_d17.37021497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.24621420.23025817X-RAY DIFFRACTION99.88
1.97-2.050.28241430.22035887X-RAY DIFFRACTION99.95
2.05-2.140.22451420.18825819X-RAY DIFFRACTION99.85
2.14-2.250.21411420.17555871X-RAY DIFFRACTION99.87
2.25-2.390.19671430.16285865X-RAY DIFFRACTION99.98
2.39-2.580.19551430.15975887X-RAY DIFFRACTION99.9
2.58-2.840.20181440.16095906X-RAY DIFFRACTION99.97
2.84-3.250.19871440.16775941X-RAY DIFFRACTION99.98
3.25-4.090.16161460.1485953X-RAY DIFFRACTION99.84
4.09-47.210.17881490.14896165X-RAY DIFFRACTION99.75
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)
10.122994928079-0.035808939609-0.1848240025680.241314428841-0.1775337436220.759519266552-0.0144431293405-0.2889442171640.3683858369670.282637122286-0.0936281961225-0.0817796860837-0.07475156800530.16501256973-0.6033237466530.32176515083-0.0561741013843-0.02385457107870.344397107711-0.1830358394210.352143307311-9.01151724302-16.1861283628-10.4300419834
21.242263849230.246223909674-0.3330654010310.44635447238-0.07073924538550.4830126318760.0495543585961-0.1852386425030.165375692214-0.0692332270896-0.0179056416034-0.316079228979-0.08155408027860.2416077604690.004114001676980.263117348016-0.004562988111810.0330589651890.2854443267160.02049844280390.3445237298067.2675031032-28.9862090409-31.9466337946
30.46331904866-0.213134858987-0.2362253262980.892334458228-0.002126153033080.3463747943780.1232444522860.138302633051-0.0826511267291-0.285183840109-0.0841769908995-0.111326228445-0.0355270375217-0.0138985991183.46137896214E-50.3087223143080.04302852418880.03310959903490.2359317402810.006943401676550.277839230781-1.08801329133-40.5583621232-42.6802697547
41.45539165567-0.227362187439-0.3537339041960.7601211294990.3415365072510.6981298324840.0682697230947-0.0456521607608-0.0725978674938-0.0340377829114-0.006359854463290.0666605553456-0.01066063026630.0035089760244-3.52742012455E-80.2480494180550.00540521627324-0.008002064775270.191852790390.03681881947130.233502057996-12.3745639199-35.0190947049-30.0313127485
50.3509980486310.0931723605769-0.1511771802470.8014988646760.2782943322020.237567123738-0.134745249141-0.622966763926-0.284308493010.005694332284990.198191952569-0.08735544781010.1443852039330.336832195272-0.06676891412390.2958857363210.0314025144044-0.0006704210777170.4551397427420.0602755375280.295946007571-11.5451941156-40.1999883607-15.5189859344
60.202570108871-0.3158767906150.4546485554391.35722115681-0.3225859028031.203899107240.0191964538867-0.253053158244-0.05037529342070.3942855491020.1159922720520.2090190375360.005493432641340.5374087867470.5278785497460.473019705750.08435172662380.1010838264470.834968888647-0.09863215432740.191552430128-25.5396225872-21.53383547590.508100197878
71.5497759212-0.756963492696-0.2205335929260.6207108269390.263121851460.456489736296-0.0536395536187-0.5561662415990.05016275185860.1276541420230.1221750187210.1269780906670.00909339683603-0.04038291807760.008288547049940.3129662633990.01174159973350.05186981189790.412421115426-0.002877536984120.233628985184-23.9559005574-25.609487799-12.8191915922
80.0191751015505-0.006618667573090.01124236205190.04868108977610.001041753249030.004223174682070.2298756137420.1820671795280.35682049692-0.118785123579-0.4608628518390.364644416585-0.299947974851-0.216394892783-1.28777034442E-50.7111957120780.174721269605-0.01311411736861.08560287960.003243275881040.498170682131-3.85572367328-21.96157359743.88954249345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 14:32)
2X-RAY DIFFRACTION2(chain A and resid 33:149)
3X-RAY DIFFRACTION3(chain A and resid 150:229)
4X-RAY DIFFRACTION4(chain A and resid 230:326)
5X-RAY DIFFRACTION5(chain A and resid 327:346)
6X-RAY DIFFRACTION6(chain A and resid 347:363)
7X-RAY DIFFRACTION7(chain A and resid 364:501)
8X-RAY DIFFRACTION8(chain A and resid 502:508)

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