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- PDB-6hsw: A CE15 glucuronoyl esterase from Teredinibacter turnerae T7901 -

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Basic information

Entry
Database: PDB / ID: 6hsw
TitleA CE15 glucuronoyl esterase from Teredinibacter turnerae T7901
ComponentsCarbohydrate esterase family 15 domain protein
KeywordsHYDROLASE / CE15 / carbohydrate esterase / glucuronoyl esterase / xylan
Function / homologyGlucuronyl esterase, fungi / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BROMIDE ION / DI(HYDROXYETHYL)ETHER / Carbohydrate esterase family 15 domain protein
Function and homology information
Biological speciesTeredinibacter turnerae T7901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14734381231 Å
AuthorsMazurkewich, S. / Lo Leggio, L. / Navarro Poulsen, J.C. / Larsbrink, J.
Funding support Sweden, Denmark, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationWood Science Center Sweden
Novo Nordisk FoundationNNF17OC0027698 Denmark
European UnionInterreg-programmet for Oresund-Kattegat-Skagerrak Denmark
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure-function analyses reveal that a glucuronoyl esterase fromTeredinibacter turneraeinteracts with carbohydrates and aromatic compounds.
Authors: Arnling Baath, J. / Mazurkewich, S. / Poulsen, J.N. / Olsson, L. / Lo Leggio, L. / Larsbrink, J.
History
DepositionOct 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Carbohydrate esterase family 15 domain protein
B: Carbohydrate esterase family 15 domain protein
C: Carbohydrate esterase family 15 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,42541
Polymers144,2443
Non-polymers3,18138
Water14,790821
1
A: Carbohydrate esterase family 15 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,03012
Polymers48,0811
Non-polymers94911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbohydrate esterase family 15 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,66319
Polymers48,0811
Non-polymers1,58218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carbohydrate esterase family 15 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,73210
Polymers48,0811
Non-polymers6519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.173, 121.173, 198.203
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-856-

HOH

21A-880-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Carbohydrate esterase family 15 domain protein


Mass: 48081.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae T7901 (bacteria)
Gene: TERTU_0517 / Plasmid: Modified pET28-a / Details (production host): contains TEV protease site / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5BN23

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Non-polymers , 6 types, 859 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution with 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer system 1 ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution with 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer system 1 (Imidazole; MES) , and 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG8000)
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.147→44.81 Å / Num. obs: 92246 / % possible obs: 99.79 % / Redundancy: 20.3 % / Biso Wilson estimate: 39.8514198624 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1978 / Rpim(I) all: 0.04459 / Rrim(I) all: 0.2028 / Net I/σ(I): 13.86
Reflection shellResolution: 2.147→2.224 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 9051 / CC1/2: 0.634 / Rpim(I) all: 0.4095 / % possible all: 98.96

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIX1.12_2829refinement
RefinementMethod to determine structure: SAD / Resolution: 2.14734381231→44.81 Å / SU ML: 0.254587693418 / Cross valid method: FREE R-VALUE / σ(F): 1.34354230713 / Phase error: 23.1248739467
RfactorNum. reflection% reflection
Rfree0.212075397524 969 1.05060011059 %
Rwork0.163563910249 --
obs0.164076629898 92233 99.8117025766 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.6282588945 Å2
Refinement stepCycle: LAST / Resolution: 2.14734381231→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9644 0 199 821 10664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011249136532810137
X-RAY DIFFRACTIONf_angle_d1.0553762109213757
X-RAY DIFFRACTIONf_chiral_restr0.05788782830111446
X-RAY DIFFRACTIONf_plane_restr0.008281833914211819
X-RAY DIFFRACTIONf_dihedral_angle_d13.1198170285871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1473-2.26060.2742652250391360.24580450114212823X-RAY DIFFRACTION99.1507268554
2.2606-2.40220.2630620508771370.21307332711112889X-RAY DIFFRACTION99.7931509998
2.4022-2.58760.2474139585461370.1900968170712952X-RAY DIFFRACTION99.8855311355
2.5876-2.8480.2130944039611380.18077883986412957X-RAY DIFFRACTION99.9465730423
2.848-3.260.2257109931471380.16945187778213039X-RAY DIFFRACTION99.9848243418
3.26-4.10690.1797857775751390.14356140171113096X-RAY DIFFRACTION99.9773379665
4.1069-46.38190.2046499979221440.14533111522613508X-RAY DIFFRACTION99.934119025

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