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- PDB-8trx: Crystal structure of a CE15 glucuronoyl esterase from Piromyces r... -

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Basic information

Entry
Database: PDB / ID: 8trx
TitleCrystal structure of a CE15 glucuronoyl esterase from Piromyces rhizinflatus
ComponentsCE15 glucuronoyl esterase
KeywordsHYDROLASE / carbohydrate / esterase / glucuronyl esterase / rumen
Biological speciesPiromyces rhizinflatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsGruninger, R.J. / Jones, D.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other government Canada
CitationJournal: Protein J. / Year: 2024
Title: Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen.
Authors: Gruninger, R.J. / Kevorkova, M. / Low, K.E. / Jones, D.R. / Worrall, L. / McAllister, T.A. / Abbott, D.W.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CE15 glucuronoyl esterase
B: CE15 glucuronoyl esterase


Theoretical massNumber of molelcules
Total (without water)92,2112
Polymers92,2112
Non-polymers00
Water1,49583
1
A: CE15 glucuronoyl esterase


Theoretical massNumber of molelcules
Total (without water)46,1061
Polymers46,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CE15 glucuronoyl esterase


Theoretical massNumber of molelcules
Total (without water)46,1061
Polymers46,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.680, 139.680, 125.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CE15 glucuronoyl esterase


Mass: 46105.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tagged construct / Source: (gene. exp.) Piromyces rhizinflatus (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 4.19 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 20% PEG10000, 100 mM HEPES, pH 7.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.00334 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2019
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00334 Å / Relative weight: 1
ReflectionResolution: 2.54→46.745 Å / Num. obs: 45952 / % possible obs: 99.96 % / Redundancy: 10.4 % / Biso Wilson estimate: 59.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08133 / Rrim(I) all: 0.08558 / Net I/σ(I): 19.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.54-2.7110.5680.822.7680610.8580.862100
2.71-2.910.2570.4984.5669450.9380.525100
2.9-3.1110.30.282858290.9780.297100
3.11-3.3710.6810.16513.653400.9940.173100
3.37-3.6610.2050.121.6243110.9960.106100
3.66-4.0210.4030.06929.8237720.9980.073100
4.02-4.4610.7020.05437.0631150.9990.056100
4.46-510.4430.04841.0224780.9990.05100
5-46.74510.2240.03945.6461020.9990.04199.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→46.745 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 2296 5 %
Rwork0.229 --
obs0.2311 45939 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.8856 Å2
Refinement stepCycle: LAST / Resolution: 2.54→46.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5829 0 0 83 5912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015998
X-RAY DIFFRACTIONf_angle_d1.0838176
X-RAY DIFFRACTIONf_dihedral_angle_d3.1064135
X-RAY DIFFRACTIONf_chiral_restr0.061865
X-RAY DIFFRACTIONf_plane_restr0.0071082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5401-2.59530.3451420.28432703X-RAY DIFFRACTION100
2.5953-2.65560.33481430.28052714X-RAY DIFFRACTION100
2.6556-2.72210.32621430.26912713X-RAY DIFFRACTION100
2.7221-2.79560.32131440.2782737X-RAY DIFFRACTION100
2.7956-2.87790.28971430.28022708X-RAY DIFFRACTION100
2.8779-2.97080.34441420.28972715X-RAY DIFFRACTION100
2.9708-3.07690.37681440.28882725X-RAY DIFFRACTION100
3.0769-3.20010.33291430.27442716X-RAY DIFFRACTION100
3.2001-3.34570.29721430.26062725X-RAY DIFFRACTION100
3.3457-3.5220.28731430.24752730X-RAY DIFFRACTION100
3.522-3.74260.25561430.23742713X-RAY DIFFRACTION100
3.7426-4.03140.27981440.20932737X-RAY DIFFRACTION100
4.0314-4.43690.24371440.19292738X-RAY DIFFRACTION100
4.4369-5.07820.2321440.19012743X-RAY DIFFRACTION100
5.0782-6.39540.21861450.21392750X-RAY DIFFRACTION100
6.3954-46.7450.24621460.21322776X-RAY DIFFRACTION100

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