PDB-8tse: Crystal structure of a CE15 glucuronoyl esterase from Ruminococcu...

ID or keywords:

Entry

Database: PDB / ID: 8tse

Title

Crystal structure of a CE15 glucuronoyl esterase from Ruminococcus flavefaciens

Components

Multidomain esterase

Keywords

HYDROLASE / carbohydrate / esterase / CE15 / glucuronoyl esterase / rumen

Function / homology

Function and homology information

(4-O-methyl)-D-glucuronate-lignin esterase / acetylxylan esterase / acetylxylan esterase activity / phosphatidylcholine lysophospholipase activity / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region
Similarity search - Function

Biological species

Ruminococcus flavefaciens 17 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 Å

Authors

Gruninger, R.J. / Jones, D.R.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	Aug 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 18, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tse.cif.gz	103.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8tse.ent.gz	75.8 KB	Display	PDB format
PDBx/mmJSON format	8tse.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tse_validation.pdf.gz	431.1 KB	Display	wwPDB validaton report
Full document	8tse_full_validation.pdf.gz	431.5 KB	Display
Data in XML	8tse_validation.xml.gz	18.6 KB	Display
Data in CIF	8tse_validation.cif.gz	28.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/8tse ftp://data.pdbj.org/pub/pdb/validation_reports/ts/8tse	HTTPS FTP

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Related structure data

Related structure data	8truC 8trxC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Multidomain esterase

hetero molecules

48.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	51.950, 60.870, 124.990
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Multidomain esterase Mass: 48061.793 Da / Num. of mol.: 1 / Fragment: CE15 glucuronoyl esterase domain Source method: isolated from a genetically manipulated source Details: C-terminal his-tagged construct of CE15 domain Source: (gene. exp.) Ruminococcus flavefaciens 17 (bacteria) Gene: cesA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RLB8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.1 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 11% isopropanol, 20% PEG4000, 100 mM HEPES, pH 7.5 / Temp details: Room temperature

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 1.00334 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2019

Radiation

Monochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.00334 Å / Relative weight: 1

Reflection

Resolution: 1.25→47.971 Å / Num. obs: 110196 / % possible obs: 99.96 % / Redundancy: 7 % / B_iso Wilson estimate: 12.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.08816 / R_rim(I) all: 0.0953 / Net I/σ(I): 11.27

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all	R_merge(I) obs
1.25-1.36		1.85	24335	0.724	0.967	100
1.36-1.49		3.37	20316	0.885	0.584	100
1.49-1.65	7.215	6.58	17033	0.962	0.317	100	0.294
1.65-1.85	7.19	11.17	13887	0.986	0.189	100	0.175
1.58-2.11	7.19	18	11104	0.994	0.113	100	0.105
2.11-2.47	6.805	23.2	8696	0.996	0.083	100	0.077
2.47-2.96	6.73	27.5	6076	0.997	0.065	100	0.06
2.96-3.72	6.83	32.3	4246	0.999	0.05	100	0.046
3.72-5	6.47	34.3	2577	0.998	0.043	100	0.04
5-47.971	6.79	35.04	1911	0.999	0.038	99.9	0.035

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.25→47.971 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.19	5507	5 %
R_work	0.1697	-	-
obs	0.1707	110185	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 15.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.25→47.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3181	0	12	335	3528

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3332
X-RAY DIFFRACTION	f_angle_d	0.813	4534
X-RAY DIFFRACTION	f_dihedral_angle_d	3.049	1874
X-RAY DIFFRACTION	f_chiral_restr	0.079	465
X-RAY DIFFRACTION	f_plane_restr	0.005	589

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.25-1.2642	0.291	181	0.2659	3441	X-RAY DIFFRACTION	100
1.2642-1.2791	0.2484	178	0.2502	3411	X-RAY DIFFRACTION	100
1.2791-1.2947	0.2711	183	0.2578	3470	X-RAY DIFFRACTION	100
1.2947-1.3111	0.2391	181	0.2325	3453	X-RAY DIFFRACTION	100
1.3111-1.3283	0.2561	182	0.2302	3462	X-RAY DIFFRACTION	100
1.3283-1.3465	0.2415	180	0.2276	3416	X-RAY DIFFRACTION	100
1.3465-1.3658	0.2356	183	0.2197	3473	X-RAY DIFFRACTION	100
1.3658-1.3861	0.2119	182	0.2178	3456	X-RAY DIFFRACTION	100
1.3861-1.4078	0.2356	181	0.2139	3447	X-RAY DIFFRACTION	100
1.4078-1.4309	0.2368	181	0.2046	3444	X-RAY DIFFRACTION	100
1.4309-1.4556	0.2194	184	0.1982	3492	X-RAY DIFFRACTION	100
1.4556-1.482	0.1972	183	0.1958	3481	X-RAY DIFFRACTION	100
1.482-1.5105	0.2202	181	0.182	3420	X-RAY DIFFRACTION	100
1.5105-1.5414	0.2101	183	0.1689	3482	X-RAY DIFFRACTION	100
1.5414-1.5749	0.1846	182	0.1611	3472	X-RAY DIFFRACTION	100
1.5749-1.6115	0.182	182	0.1584	3456	X-RAY DIFFRACTION	100
1.6115-1.6518	0.1687	183	0.153	3470	X-RAY DIFFRACTION	100
1.6518-1.6965	0.1777	183	0.1526	3476	X-RAY DIFFRACTION	100
1.6965-1.7464	0.1699	184	0.1568	3490	X-RAY DIFFRACTION	100
1.7464-1.8028	0.18	182	0.1565	3474	X-RAY DIFFRACTION	100
1.8028-1.8672	0.1631	184	0.1551	3485	X-RAY DIFFRACTION	100
1.8672-1.942	0.1723	183	0.1607	3486	X-RAY DIFFRACTION	100
1.942-2.0304	0.1967	185	0.1631	3516	X-RAY DIFFRACTION	100
2.0304-2.1374	0.1671	184	0.1616	3492	X-RAY DIFFRACTION	100
2.1374-2.2713	0.1853	186	0.1632	3520	X-RAY DIFFRACTION	100
2.2713-2.4467	0.1854	185	0.1691	3526	X-RAY DIFFRACTION	100
2.4467-2.6929	0.1936	185	0.1723	3523	X-RAY DIFFRACTION	100
2.6929-3.0825	0.1949	190	0.1729	3592	X-RAY DIFFRACTION	100
3.0825-3.8834	0.1855	188	0.1629	3587	X-RAY DIFFRACTION	100
3.8834-47.971	0.1699	198	0.145	3765	X-RAY DIFFRACTION	100

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