PDB-6m6l: The crystal structure of glycosidase hydrolyzing Notoginsenoside

ID or keywords:

Entry

Database: PDB / ID: 6m6l

Title

The crystal structure of glycosidase hydrolyzing Notoginsenoside

Components

Beta-glucosidase

Keywords

HYDROLASE / Glycosidase / Notoginsenoside

Function / homology

Function and homology information

beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function

Biological species

Kribbella flavida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Wang, R.F.

Citation

Journal: To Be Published
Title: Characterization and Structural Elucidation of Enhanced Catalytic Activity upon Engineering Glycosidase KfGH01 for the Production of Vina-ginsenoside R7
Authors: Wang, R.F.

History

Deposition	Mar 15, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6m6l.cif.gz	213 KB	Display	PDBx/mmCIF format
PDB format	pdb6m6l.ent.gz	167.1 KB	Display	PDB format
PDBx/mmJSON format	6m6l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m6/6m6l ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m6l	HTTPS FTP

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Related structure data

Related structure data	6m6mC 3ta9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6m6m-1 1np2-1 3zjk-1 2j7f-1 2jal-1 4bce-1 1gon-1 4bce-3 6m6m-2 2o9r-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Beta-glucosidase

B: Beta-glucosidase

hetero molecules

99.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-glucosidase

hetero molecules

defined by author&software
Evidence: gel filtration
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-glucosidase

hetero molecules

defined by author&software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.608, 95.571, 93.348
Angle α, β, γ (deg.)	90.00, 90.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Beta-glucosidase

Mass: 49331.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) (bacteria)
Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_5268
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D2PL27, beta-glucosidase

#2: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION

#4: Sugar

ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose

Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₅H₁₀O₅ / Feature type: SUBJECT OF INVESTIGATION

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1185 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.28 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Sodium citrate tribasic dehydrate (pH 5.6), 0.2 M ammonium acetate and PEG 4000 (30%, w/v)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.49→50 Å / Num. obs: 147102 / % possible obs: 96.9 % / Redundancy: 3.8 % / CC_1/2: 1 / Net I/σ(I): 29.5
Reflection shell	Resolution: 1.49→1.5 Å / Num. unique obs: 147102 / CC_1/2: 1

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TA9

3ta9

Resolution: 1.5→35.371 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.93
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns

	R_factor	Num. reflection	% reflection
R_free	0.1741	7427	5.05 %
R_work	0.1498	-	-
obs	0.151	147102	99.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.5→35.371 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6953	0	32	1185	8170

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7250
X-RAY DIFFRACTION	f_angle_d	0.96	9930
X-RAY DIFFRACTION	f_dihedral_angle_d	15.613	4223
X-RAY DIFFRACTION	f_chiral_restr	0.06	1050
X-RAY DIFFRACTION	f_plane_restr	0.008	1314

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 (%)
1.5-1.517	0.202	256	0.1751	4574	X-RAY DIFFRACTION	100
1.517-1.5349	0.2091	253	0.1729	4661	X-RAY DIFFRACTION	100
1.5349-1.5536	0.1996	241	0.168	4660	X-RAY DIFFRACTION	100
1.5536-1.5733	0.2011	250	0.1694	4617	X-RAY DIFFRACTION	100
1.5733-1.594	0.2249	244	0.1644	4680	X-RAY DIFFRACTION	100
1.594-1.6158	0.1894	216	0.1589	4631	X-RAY DIFFRACTION	100
1.6158-1.6389	0.1793	211	0.149	4720	X-RAY DIFFRACTION	100
1.6389-1.6634	0.1869	235	0.1495	4643	X-RAY DIFFRACTION	100
1.6634-1.6894	0.1868	213	0.1494	4701	X-RAY DIFFRACTION	100
1.6894-1.717	0.1806	256	0.1479	4580	X-RAY DIFFRACTION	100
1.717-1.7467	0.1755	262	0.1468	4678	X-RAY DIFFRACTION	100
1.7467-1.7784	0.1429	241	0.142	4647	X-RAY DIFFRACTION	100
1.7784-1.8126	0.1794	280	0.1503	4648	X-RAY DIFFRACTION	100
1.8126-1.8496	0.1746	261	0.1503	4610	X-RAY DIFFRACTION	100
1.8496-1.8898	0.1829	237	0.1446	4661	X-RAY DIFFRACTION	100
1.8898-1.9338	0.1783	241	0.147	4664	X-RAY DIFFRACTION	100
1.9338-1.9821	0.1597	253	0.1443	4649	X-RAY DIFFRACTION	100
1.9821-2.0357	0.1771	253	0.1453	4648	X-RAY DIFFRACTION	100
2.0357-2.0956	0.185	243	0.1464	4670	X-RAY DIFFRACTION	100
2.0956-2.1633	0.1585	290	0.1428	4609	X-RAY DIFFRACTION	100
2.1633-2.2406	0.1601	254	0.1468	4633	X-RAY DIFFRACTION	100
2.2406-2.3303	0.1874	277	0.1487	4680	X-RAY DIFFRACTION	100
2.3303-2.4363	0.181	243	0.1524	4632	X-RAY DIFFRACTION	100
2.4363-2.5647	0.1685	231	0.1549	4684	X-RAY DIFFRACTION	100
2.5647-2.7253	0.1965	269	0.1646	4670	X-RAY DIFFRACTION	100
2.7253-2.9357	0.1998	265	0.169	4627	X-RAY DIFFRACTION	100
2.9357-3.2309	0.1778	250	0.1594	4674	X-RAY DIFFRACTION	100
3.2309-3.698	0.1739	185	0.1403	4718	X-RAY DIFFRACTION	99
3.698-4.6574	0.1386	265	0.1245	4658	X-RAY DIFFRACTION	99
4.6574-35.3	0.1445	252	0.1493	4748	X-RAY DIFFRACTION	99

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