PDB-7lr2: Crystal structure of GH5_18 from Bifidobacterium longum subsp. lo...

ID or keywords:

Entry

Database: PDB / ID: 7lr2

Title

Crystal structure of GH5_18 from Bifidobacterium longum subsp. longum ATCC 55813 in complex with GlcNAc

Components

Glycosyl hydrolase BlGH5_18

Keywords

HYDROLASE / Glycosidase / N-glycan / CAZyme

Function / homology

Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Glycosyl hydrolase

Function and homology information

Biological species

Bifidobacterium longum subsp. longum ATCC 55813 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Higgins, M.A. / Ryan, K.S.

Funding support

Canada, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2021
Title: N-Glycan Degradation Pathways in Gut- and Soil-Dwelling Actinobacteria Share Common Core Genes.
Authors: Higgins, M.A. / Tegl, G. / MacDonald, S.S. / Arnal, G. / Brumer, H. / Withers, S.G. / Ryan, K.S.

History

Deposition	Feb 15, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 18, 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	7lr2.cif.gz	822 KB	Display	PDBx/mmCIF format
PDB format	pdb7lr2.ent.gz	565.8 KB	Display	PDB format
PDBx/mmJSON format	7lr2.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/lr/7lr2 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/7lr2	HTTPS FTP

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Related structure data

Related structure data	7lqxC 7lr1SC 7lr6C 7lr7C 7lr8C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7lr6-1 7lr1-1 7lr1-2 6mpc-d 7lr8-d 7lr7-1 3sae-d 3sdr-d 7lr6-2 4zb9-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycosyl hydrolase BlGH5_18

B: Glycosyl hydrolase BlGH5_18

C: Glycosyl hydrolase BlGH5_18

D: Glycosyl hydrolase BlGH5_18

hetero molecules

202 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Glycosyl hydrolase BlGH5_18

hetero molecules

A: Glycosyl hydrolase BlGH5_18

hetero molecules

defined by author&software
Evidence: gel filtration
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glycosyl hydrolase BlGH5_18

hetero molecules

B: Glycosyl hydrolase BlGH5_18

hetero molecules

defined by author&software
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	105.559, 143.486, 155.893
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein

Glycosyl hydrolase BlGH5_18

Mass: 49622.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bifidobacterium longum subsp. longum ATCC 55813 (bacteria)
Gene: HMPREF0175_1989 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C2GY91

#2: Chemical

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

Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C₂H₆O₂

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.97 Å³/Da / Density % sol: 58.64 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.22 M ammonium phosphate monobasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.4→39.09 Å / Num. obs: 92362 / % possible obs: 99.3 % / Redundancy: 13.5 % / B_iso Wilson estimate: 44.49 Å² / CC_1/2: 0.996 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.4→2.44 Å / Num. unique obs: 4443 / CC_1/2: 0.681

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7LR1

7lr1

Resolution: 2.4→38.97 Å / SU ML: 0.3154 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1495 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2239	4796	5.22 %
R_work	0.1723	87088	-
obs	0.1749	91884	98.78 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→38.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13201	0	194	726	14121

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	13805
X-RAY DIFFRACTION	f_angle_d	0.8968	18836
X-RAY DIFFRACTION	f_chiral_restr	0.0518	2001
X-RAY DIFFRACTION	f_plane_restr	0.0061	2453
X-RAY DIFFRACTION	f_dihedral_angle_d	5.1348	10868

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 (%)
2.4-2.43	0.4136	132	0.3266	2744	X-RAY DIFFRACTION	94.67
2.43-2.46	0.3353	142	0.2488	2767	X-RAY DIFFRACTION	94.91
2.46-2.49	0.3161	156	0.2337	2769	X-RAY DIFFRACTION	95.56
2.49-2.52	0.3083	174	0.2439	2878	X-RAY DIFFRACTION	98.52
2.52-2.55	0.3047	177	0.2375	2855	X-RAY DIFFRACTION	99.7
2.55-2.59	0.2967	168	0.2238	2887	X-RAY DIFFRACTION	99.97
2.59-2.62	0.2549	164	0.2175	2914	X-RAY DIFFRACTION	99.84
2.62-2.66	0.3138	176	0.222	2913	X-RAY DIFFRACTION	99.94
2.66-2.7	0.2737	172	0.2125	2891	X-RAY DIFFRACTION	99.97
2.7-2.75	0.2799	181	0.2027	2874	X-RAY DIFFRACTION	100
2.75-2.79	0.2601	148	0.206	2934	X-RAY DIFFRACTION	99.97
2.79-2.85	0.2997	157	0.2041	2901	X-RAY DIFFRACTION	99.8
2.85-2.9	0.2799	154	0.2115	2907	X-RAY DIFFRACTION	99.38
2.9-2.96	0.3118	150	0.2072	2933	X-RAY DIFFRACTION	99.71
2.96-3.02	0.2525	156	0.2087	2912	X-RAY DIFFRACTION	99.68
3.02-3.09	0.308	153	0.2021	2909	X-RAY DIFFRACTION	99.61
3.09-3.17	0.2467	178	0.1952	2889	X-RAY DIFFRACTION	99.61
3.17-3.26	0.2221	153	0.1948	2923	X-RAY DIFFRACTION	99.58
3.26-3.35	0.2598	162	0.1914	2909	X-RAY DIFFRACTION	99.45
3.35-3.46	0.2511	167	0.2023	2882	X-RAY DIFFRACTION	98.45
3.46-3.58	0.2441	172	0.1865	2769	X-RAY DIFFRACTION	94.6
3.58-3.73	0.2257	143	0.1754	2913	X-RAY DIFFRACTION	98.77
3.73-3.9	0.2066	161	0.1552	2950	X-RAY DIFFRACTION	99.46
3.9-4.1	0.1975	160	0.1373	2951	X-RAY DIFFRACTION	99.65
4.1-4.36	0.1825	173	0.1287	2918	X-RAY DIFFRACTION	99.65
4.36-4.7	0.1608	174	0.1174	2939	X-RAY DIFFRACTION	99.43
4.7-5.17	0.1672	155	0.1278	2975	X-RAY DIFFRACTION	99.37
5.17-5.91	0.1777	133	0.1456	3001	X-RAY DIFFRACTION	98.68
5.91-7.44	0.2081	150	0.159	2959	X-RAY DIFFRACTION	97.4
7.44-38.97	0.1544	155	0.1558	3122	X-RAY DIFFRACTION	98.11

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	4.31222805837	0.390441568245	-0.351932724716	2.54463714864	-0.0196164752315	2.40659832907	-0.177614292961	0.311258971216	0.0254700762185	-0.160590038803	0.00823312126263	0.0213961113827	0.0294759202225	-0.134537134039	0.189754657963	0.339614796646	-0.0131581413391	-0.0232703482668	0.624269796508	0.081584823574	0.427583414657	-20.1592086254	3.76752932313	-5.83921335883
2	7.1763626215	-2.61567730831	-2.37797782144	1.76320039227	-0.0795515024538	5.1852007516	0.211196493558	-0.00102805838561	0.445323926892	-0.0971775087593	-0.0090053265413	0.0478787104849	-0.492694021225	0.226322782172	-0.197025411251	0.320397738565	-0.090515057736	0.0211045463635	0.313443453829	0.0457561053859	0.328646419605	-53.0055722765	6.8098142377	10.2591496568
3	1.4335423377	-0.257046188123	-0.606112383244	0.754824110802	-0.021873498906	2.60095185239	-0.038940997127	-0.0573189076054	-0.169857689943	0.1280386532	-0.112800494673	0.0581060474897	0.12696169714	0.00762502607192	0.147828398733	0.264572908494	-0.00826872856668	-0.0043644419568	0.256110392785	0.0025151453023	0.301109410675	-63.1839794932	-3.56690995636	21.0649819026
4	2.03012169596	-0.112269363668	-0.303010637908	2.95343221154	0.410479444064	1.88020503205	-0.0949614355293	-0.16158117634	-0.0604828830449	0.168713513322	0.0433487152893	-0.0875180991574	0.108535342718	0.224058311609	0.0584382487722	0.266488908188	0.0450214643218	0.0086755593129	0.328444873794	0.0380533050394	0.258066829992	-43.7844493274	-8.80015375381	19.5961797831
5	1.67085398546	-0.144904674142	-0.662742301501	5.08390133735	-1.69063352889	3.3693208262	0.200158433393	0.148675905915	0.199219936216	-0.738211903947	-0.156399446604	0.0672536316692	-0.269981090577	0.273475426057	-0.028761775172	0.272722351334	-0.0410879541822	-0.0273167137399	0.494315490089	0.0794962461875	0.411932411605	-39.3216174696	-0.576432319541	10.1530166248
6	1.82504676112	-0.504016817732	-0.448986680932	3.20158937443	0.415072168747	1.79638178119	-0.070837142437	-0.151279897207	-0.124713849416	0.13908033916	-0.010248397537	-0.0169410120575	0.368934134347	0.218975497394	0.0395198474984	0.46722028423	0.114073210849	-0.0449502166612	0.477417949934	0.116175826654	0.384973306383	-38.0784236516	-22.6800381702	26.4203954384
7	2.73629683726	0.956549983925	0.0450464291755	2.18006527592	-0.062713895848	1.30251154146	0.117006305254	-0.0552980324701	0.113367090264	0.105785072165	-0.0399700050131	0.0111144821315	-0.104642217441	0.0115438693614	-0.0691684798512	0.295306528238	0.0293702054237	0.0120046574101	0.323942221993	0.0243500427488	0.250502887037	-33.9447754857	-51.3321156084	47.9397480302
8	1.23394920196	-0.229358682415	-0.0779496950993	1.01489500694	-0.371034528454	2.17769969045	0.0463485383918	0.0222278644858	0.112128312578	-0.0581855260499	-0.00598946543668	0.00235754113038	-0.15456913527	0.0252011807544	-0.0425835186384	0.348602892062	0.0144457233881	0.0108371898609	0.3610782317	0.0521945915048	0.350667881935	-22.9277627988	-51.6406515708	31.0696608727
9	5.15294916882	-0.366105423493	-0.0677666617684	7.7265091566	0.377050605935	2.64596493429	0.13671071503	0.261840263205	0.176270049824	-0.255666394744	-0.190989676798	0.0345666082002	0.113608290024	0.271064739865	0.0785234662376	0.391642268211	0.0241446880752	0.000786335581215	0.493151830608	0.0107409511654	0.262322067848	-21.9645749743	-48.9579042982	15.7174405467
10	4.64428120901	-2.24841614898	-0.460583549267	2.09346471737	-1.81525241388	4.54555776337	-0.0488590059232	-0.326093444995	-0.0928684126046	0.131210225003	0.00496236990238	0.162307901907	0.284503545006	0.0837978917226	-0.0182203858482	0.333837256877	-0.0183090357757	0.0625818676787	0.281827243489	-0.0702855438026	0.328853364686	12.7988935916	-14.98254597	71.4952799902
11	1.83924261852	0.16787145526	0.372471686937	0.809174501442	0.00878744824569	0.661361714194	-0.00259345942158	0.19172695985	-0.376315345883	0.00678859916441	0.0971599287549	-0.0695059187806	0.197668053059	0.0896521963796	-0.0767794789402	0.41526468304	-0.00510177946267	0.0123782477969	0.351523756452	-0.116427512093	0.452493936498	24.5666183424	-23.6661202154	65.1142556587
12	2.85484351302	-0.786371802148	-1.02989574983	2.16527700622	0.0356682997136	3.0862646334	-0.106014828225	0.537576051569	-0.36534401285	-0.450756138738	-0.0175690020094	-0.0826110718021	-0.0958611090196	0.225763560158	0.0755871429609	0.58058801567	-0.0119104595225	-0.0247126784466	0.616413184333	-0.24782850105	0.613128882166	29.9655892701	-24.5426180093	49.6372340468
13	0.607217547567	0.0232462051345	0.043139605545	1.36031232284	0.0975866196918	1.88243323397	-0.0230879078109	0.289153886036	-0.257707766547	-0.148236492238	0.0709503913814	0.0469128554198	0.304310385561	-0.274761544129	-0.045401990622	0.345851103314	-0.0911147854965	0.00225790570901	0.456182678408	-0.122309294014	0.396755413373	10.2383709676	-14.0716607852	49.9115182727
14	5.11821372864	-0.0211958649908	-1.09262063511	6.47515666497	-2.15300700768	1.93897286211	-0.0707078064091	0.342331021772	-0.312927937699	-0.559108715309	0.131618653548	-0.0288603885085	0.260327133427	-0.10834086712	-0.084929521372	0.485500757315	-0.118463612563	0.0387463841126	0.7060368777	-0.204420397998	0.383765777898	10.3741813005	-17.4432574754	34.4330348115
15	2.06097258726	-0.750801223447	-0.893412419199	1.61333269877	2.20247792952	5.43191668224	0.131760453206	-0.196193919491	0.453225276956	0.114138777596	-0.00215480353832	-0.0722579933266	-0.418849955994	0.158743344788	-0.0984036358822	0.402612306466	0.0465647422163	-0.0445975729088	0.380378575001	0.00410600232294	0.383276397165	8.26534112717	20.2307067849	8.18200434845
16	1.82609894567	-0.2309842031	-0.614501506193	1.23867382701	0.726613962177	2.23655691301	-0.122433629042	0.16747203036	-0.0578163767575	-0.0701675307949	0.0358856142682	0.102750195551	-0.00873775914917	0.0359410625025	0.0790833264165	0.292907061877	-0.0154719735836	-0.0126689541068	0.340605066256	0.0560992847574	0.313492868123	10.9736964541	6.15134564149	-2.48014780767
17	3.03066761926	0.609018940992	-0.182560241247	1.72310072224	0.522909638868	1.08738661298	-0.165877810129	0.192499604672	0.218361278339	-0.0444018282775	0.136887383604	0.277377604353	-0.0934029605319	-0.285217231251	0.023772986977	0.333837766708	0.0274885335345	-0.0147683007429	0.533880730946	0.0614834888016	0.380143947412	-7.95199634978	11.8397836559	-0.974005508963
18	1.3450293883	0.461273675609	0.19811883181	4.24746087253	-1.98050899743	7.42263061266	-0.0519834511942	0.0395325322841	0.639407081717	0.502099398786	-0.00349898926286	0.020098623001	-0.851106626362	-0.49517133379	0.0919106504116	0.365847100977	0.114871240126	-0.0672232740763	0.510889220206	-0.0628775644635	0.668003271312	-4.04156749359	25.9482973554	6.64174704238

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 332 through 422 )	A	A	332 - 422	332 - 422
2	2	chain 'B' and (resid -1 through 34 )	B	B	-1 - 34	-1 - 34
3	3	chain 'B' and (resid 35 through 171 )	B	B	35 - 171	35 - 171
4	4	chain 'B' and (resid 172 through 302 )	B	B	172 - 302	172 - 302
5	5	chain 'B' and (resid 303 through 341 )	B	B	303 - 341	303 - 341
6	6	chain 'B' and (resid 342 through 422 )	B	B	342 - 422	342 - 422
7	7	chain 'C' and (resid 0 through 144 )	C	C	0 - 144	0 - 144
8	8	chain 'C' and (resid 145 through 375 )	C	C	145 - 375	145 - 375
9	9	chain 'C' and (resid 376 through 422 )	C	C	376 - 422	376 - 422
10	10	chain 'D' and (resid 0 through 34 )	D	D	0 - 34	0 - 34
11	11	chain 'D' and (resid 35 through 144 )	D	D	35 - 144	10 - 70
12	12	chain 'D' and (resid 145 through 171 )	D	D	145 - 171	145 - 171
13	13	chain 'D' and (resid 172 through 375 )	D	D	172 - 375	172 - 375
14	14	chain 'D' and (resid 376 through 422 )	D	D	376 - 422	376 - 422
15	15	chain 'A' and (resid 0 through 34 )	A	A	0 - 34	0 - 34
16	16	chain 'A' and (resid 35 through 168 )	A	A	35 - 168	35 - 168
17	17	chain 'A' and (resid 169 through 302 )	A	A	169 - 302	169 - 302
18	18	chain 'A' and (resid 303 through 331 )	A	A	303 - 331	303 - 331

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