PDB-9fyl: Lacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bou...

ID or keywords:

Entry

Database: PDB / ID: 9fyl

Title

Lacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bound in active site

Components

Glycoside hydrolase family 20 catalytic domain-containing protein

Keywords

HYDROLASE / lacto-N-biosidase / GH20

Function / homology

Hexosaminidase D-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / beta-N-acetylhexosaminidase activity / : / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glycoside hydrolase family 20 catalytic domain-containing protein

Function and homology information

Biological species

Treponema denticola ATCC 35405 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.24 Å

Authors

Vuillemin, M. / Siebenhaar, S. / Zeuner, B. / Morth, J.P.

Funding support

Denmark, 1items

Citation

Journal: Chembiochem / Year: 2024
Title: Discovery of Lacto-N-biosidases and a Novel N-Acetyllactosaminidase Activity in the CAZy Family GH20: Functional Diversity and Structural Insights.
Authors: Vuillemin, M. / Muschiol, J. / Zhang, Y. / Holck, J. / Barrett, K. / Morth, J.P. / Meyer, A.S. / Zeuner, B.

History

Deposition	Jul 3, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fyl.cif.gz	472.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9fyl.ent.gz	328.3 KB	Display	PDB format
PDBx/mmJSON format	9fyl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fyl_validation.pdf.gz	440.6 KB	Display	wwPDB validaton report
Full document	9fyl_full_validation.pdf.gz	460.7 KB	Display
Data in XML	9fyl_validation.xml.gz	30.4 KB	Display
Data in CIF	9fyl_validation.cif.gz	38.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/9fyl ftp://data.pdbj.org/pub/pdb/validation_reports/fy/9fyl	HTTPS FTP

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Related structure data

Related structure data	9fymC 9fynC 9fyoC 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: Glycoside hydrolase family 20 catalytic domain-containing protein

B: Glycoside hydrolase family 20 catalytic domain-containing protein

hetero molecules

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

1

A: Glycoside hydrolase family 20 catalytic domain-containing protein

hetero molecules

defined by author
Evidence: gel filtration, elute as a monomer in gel filtration
38 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycoside hydrolase family 20 catalytic domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.917, 89.471, 93.757
Angle α, β, γ (deg.)	90.000, 127.000, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 38 through 64 or resid 67...
d_2	ens_1	(chain "B" and (resid 38 through 64 or resid 67...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	LYS	LYS	GLN	GLN	A	A	38 - 64	5 - 31
d_1	2	GLY	GLY	ASN	ASN	A	A	67 - 89	34 - 56
d_1	3	TYR	TYR	ASN	ASN	A	A	91 - 215	58 - 182
d_1	4	LEU	LEU	TYR	TYR	A	A	217 - 246	184 - 213
d_1	5	GLY	GLY	ILE	ILE	A	A	248 - 302	215 - 269
d_1	6	ALA	ALA	ASN	ASN	A	A	304 - 334	271 - 301
d_1	7	ASN	ASN	SER	SER	A	A	336 - 338	303 - 305
d_1	8	TYR	TYR	HIS	HIS	A	A	340 - 362	307 - 329
d_2	1	LYS	LYS	GLN	GLN	B	B	38 - 64	5 - 31
d_2	2	GLY	GLY	ASN	ASN	B	B	67 - 89	34 - 56
d_2	3	TYR	TYR	ASN	ASN	B	B	91 - 215	58 - 182
d_2	4	LEU	LEU	TYR	TYR	B	B	217 - 246	184 - 213
d_2	5	GLY	GLY	ILE	ILE	B	B	248 - 302	215 - 269
d_2	6	ALA	ALA	ASN	ASN	B	B	304 - 334	271 - 301
d_2	7	ASN	ASN	SER	SER	B	B	336 - 338	303 - 305
d_2	8	TYR	TYR	HIS	HIS	B	B	340 - 362	307 - 329

NCS oper: (Code: givenMatrix: (-0.272046913077, -0.0296320066868, -0.961827646341), (0.0179980201791, -0.999507612231, 0.0257022248341), (-0.96211566267, -0.0103187824623, 0.272446277959)Vector: 12. ...

#1: Protein	Glycoside hydrolase family 20 catalytic domain-containing protein Mass: 37972.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Peptide signal has been removed and linker "LE" and 6xHis-Tag has been added at the C-terminus of the protein Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria) Gene: TDE_1723 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73LY9
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.84 Å³/Da / Density % sol: 56.74 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% w/v PEG 8000, 9% ethylene glycol, 0.1M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.24→46.31 Å / Num. obs: 40862 / % possible obs: 99.79 % / Redundancy: 6.8 % / B_iso Wilson estimate: 71.65 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.07793 / R_rim(I) all: 0.08431 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.24→2.32 Å / R_merge(I) obs: 1 / Num. unique obs: 4044 / CC_1/2: 0.323 / R_rim(I) all: 1

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
autoPROC		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.24→46.31 Å / SU ML: 0.4749 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.6937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2689	1990	4.88 %
R_work	0.2319	38749	-
obs	0.2338	40739	99.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 103.99 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→46.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5274	0	2	33	5309

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0148	5408
X-RAY DIFFRACTION	f_angle_d	1.4502	7318
X-RAY DIFFRACTION	f_chiral_restr	0.117	782
X-RAY DIFFRACTION	f_plane_restr	0.0147	934
X-RAY DIFFRACTION	f_dihedral_angle_d	8.9956	714

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.791446732607 Å

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 (%)
2.24-2.3	0.5616	139	0.4895	2704	X-RAY DIFFRACTION	97.93
2.3-2.36	0.4717	141	0.4524	2740	X-RAY DIFFRACTION	99.14
2.36-2.43	0.4498	138	0.4114	2734	X-RAY DIFFRACTION	99.51
2.43-2.51	0.3904	143	0.3599	2762	X-RAY DIFFRACTION	99.9
2.51-2.6	0.3769	143	0.3682	2782	X-RAY DIFFRACTION	99.93
2.6-2.7	0.4263	143	0.3783	2765	X-RAY DIFFRACTION	99.79
2.7-2.82	0.4055	141	0.3325	2757	X-RAY DIFFRACTION	99.97
2.82-2.97	0.3599	142	0.2909	2750	X-RAY DIFFRACTION	99.93
2.97-3.16	0.3413	142	0.2816	2795	X-RAY DIFFRACTION	99.97
3.16-3.4	0.3036	143	0.3007	2757	X-RAY DIFFRACTION	99.83
3.4-3.75	0.2792	143	0.2278	2788	X-RAY DIFFRACTION	99.69
3.75-4.29	0.2366	142	0.206	2776	X-RAY DIFFRACTION	99.97
4.29-5.4	0.2072	145	0.1843	2795	X-RAY DIFFRACTION	99.93
5.4-46.31	0.2214	145	0.177	2844	X-RAY DIFFRACTION	99.53

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.584252906717	-0.162097152568	-0.516612656247	1.34827349888	0.539056653317	3.03094180048	-0.0266643306924	-0.45662778205	1.02673568266	0.0793189130878	-0.00386991644219	0.131517223534	-1.42666632535	0.0858007530227	0.00140291477603	1.23163775017	0.112332887355	-0.0102544961134	0.874757332545	-0.0988202358358	1.10563800052	38.4732567144	16.6683796015	14.2400089335
2	0.293092675521	5.71237827776E-5	-0.293414053777	0.362825515503	0.308954368256	0.37181283522	0.290783009787	0.354782393628	0.524360399374	-0.516780747769	0.0300927082644	0.311254494439	-0.784730462337	0.0844633558696	0.00066697280846	0.788953590159	-0.0332074469196	0.135246368956	0.946930177989	0.119435982526	0.857760661682	52.2988596666	6.48155674025	-1.66062665142
3	2.98367898489	-1.06893470622	-0.2100351381	2.52142533435	-0.668456218628	2.28110552516	-0.0445499224403	0.141471141346	-0.273950792394	-0.119639436798	0.0865507446353	0.453995566691	-0.0262577348231	-0.127877658678	-0.000236229427859	0.58057765641	0.0417422553312	-0.0156473886654	0.72896704229	0.0260413273176	0.82410104993	36.7986599262	-1.39718420597	3.32340221819
4	0.243679641892	-0.0162168800346	0.63125716604	0.600739452563	0.340602618834	1.39281734642	-0.576461250337	-0.43271187432	0.666806835424	-0.536015443971	0.381508987142	0.717401362848	-1.35052793146	-0.539397261834	-0.0241734254747	0.777366552818	0.163488748303	0.0844468604125	0.949722824532	0.168150861914	1.2150961583	27.029131132	13.1646293814	6.01730900473
5	0.0706456422287	-0.0250660160889	-0.208132265769	0.487835172647	0.388713901497	0.280856104456	0.0703990190661	0.233838609651	-0.518360477936	0.777414805907	-1.16579916015	0.261848872676	-0.636503144707	0.351384037786	-0.0260536551234	1.2668014393	0.295277546624	0.038028437152	1.31480686851	0.248412892765	1.83294006904	13.8331653455	15.2363444228	16.2347107909
6	2.39834122269	0.51881401853	-0.551649319149	3.76396518751	-0.806875563249	3.78554380737	-0.127989056747	-0.0311240301335	-0.68099763935	0.241207790406	0.234444643445	0.306714323715	0.916648834289	-0.525501616416	0.000850603816729	1.0558182119	0.00255042550462	0.0745339970292	0.882581750091	0.0842429420197	0.850394203536	-8.09018285961	21.4541281798	28.0760486571
7	0.324086035981	-0.291193447426	0.526622970633	1.10453703651	-0.341389990376	0.667775619159	0.206834063621	-0.028113975782	0.331992120754	0.684798083821	0.170973447958	0.090722104087	-0.729532838006	-0.157151373295	0.000992242391059	0.694624330266	0.105609449719	0.0661930511701	0.922716733038	0.0775410387036	0.77435633991	-3.04419698636	40.2857513582	22.7475235462
8	0.433680992709	0.377615542229	-0.529109369121	2.19708035591	-0.657139766693	2.46346915569	-0.290520060553	-0.534586123775	-0.0256429588247	1.19873336737	0.196476692679	-0.543097900333	-0.154303222047	0.298062509089	-0.000211178721328	1.18724217145	0.215263157356	-0.0753377450336	0.990728169565	0.0315288894942	0.921633337491	3.01313553483	35.1942694834	37.9334295992
9	1.78982024972	1.24152378787	-0.196469495792	0.875061454728	-0.125896044263	0.600469740697	0.119620765401	-0.415272724822	-0.547080122042	1.14624057329	0.23673207284	-0.343038961751	0.709376394796	0.251481831848	-0.00227853277367	1.66745314369	0.308450077824	-0.107467161639	1.09453617364	0.056135067927	0.865711462591	1.71220733959	22.9669272409	45.4073261712
10	0.18792587873	0.388102359812	-0.215725932633	0.424785626423	-0.265364080439	0.219297113789	0.130335382339	-0.419440681756	-0.370428485119	0.0730711967267	-0.557204239313	0.29542807453	-0.546059074028	0.254170452085	-0.00159917174757	2.05698687875	0.343477755328	0.0730675085767	1.30814433817	0.166893398102	1.09630084663	-7.03704192642	16.3363704327	59.1139359856

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 38 through 115 )	A	A	38 - 115	1 - 78
2	2	chain 'A' and (resid 116 through 148 )	A	A	116 - 148	79 - 111
3	3	chain 'A' and (resid 149 through 315 )	A	A	149 - 315	112 - 278
4	4	chain 'A' and (resid 316 through 340 )	A	A	316 - 340	279 - 303
5	5	chain 'A' and (resid 341 through 362 )	A	A	341 - 362	304 - 325
6	6	chain 'B' and (resid 38 through 194 )	B	E	38 - 194	1 - 157
7	7	chain 'B' and (resid 195 through 221 )	B	E	195 - 221	158 - 184
8	8	chain 'B' and (resid 222 through 289 )	B	E	222 - 289	185 - 252
9	9	chain 'B' and (resid 290 through 340 )	B	E	290 - 340	253 - 303
10	10	chain 'B' and (resid 341 through 362 )	B	E	341 - 362	304 - 325

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