PDB-7lr8: Crystal structure of GH5_18-E153A from Streptomyces cattleya in c...

ID or keywords:

Entry

Database: PDB / ID: 7lr8

Title

Crystal structure of GH5_18-E153A from Streptomyces cattleya in complex with Manb1-4GlcNAc

Components

Uncharacterized protein ScGH5_18

Keywords

HYDROLASE / Glycosidase / N-glycan / CAZyme

Function / homology

Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 2-(2-ETHOXYETHOXY)ETHANOL / Glycosyl hydrolase

Function and homology information

Biological species

Streptomyces cattleya (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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 16, 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	7lr8.cif.gz	427.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7lr8.ent.gz	288.9 KB	Display	PDB format
PDBx/mmJSON format	7lr8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7lr8_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7lr8_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7lr8_validation.xml.gz	39.7 KB	Display
Data in CIF	7lr8_validation.cif.gz	60.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/7lr8 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/7lr8	HTTPS FTP

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Related structure data

Related structure data	7lqxC 7lr1C 7lr2C 7lr6C 7lr7SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7lr6-1 7lr7-1 7lr1-1 7lr2-1 4zb9-d 2jiu-d 3sdr-d 2vme-2 1zjc-1 6mpc-d 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: Uncharacterized protein ScGH5_18

B: Uncharacterized protein ScGH5_18

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	152.869, 76.455, 79.920
Angle α, β, γ (deg.)	90.000, 117.240, 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

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

Uncharacterized protein ScGH5_18

Mass: 47858.348 Da / Num. of mol.: 2 / Mutation: E153A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_p07120 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F8JJ04

#2: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 836 molecules

#3: Chemical	ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL Mass: 134.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.17 Å³/Da / Density % sol: 43.29 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 28% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris pH 8.5

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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: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.6→38.98 Å / Num. obs: 106029 / % possible obs: 98.5 % / Redundancy: 6.9 % / B_iso Wilson estimate: 18.13 Å² / CC_1/2: 0.999 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5114 / CC_1/2: 0.935

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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: 7LR7

7lr7

Resolution: 1.6→38.98 Å / SU ML: 0.1727 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7933 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.1906	5393	5.09 %
R_work	0.1617	100491	-
obs	0.1632	105884	98.27 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→38.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6410	0	98	829	7337

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	6842
X-RAY DIFFRACTION	f_angle_d	0.8256	9402
X-RAY DIFFRACTION	f_chiral_restr	0.055	1021
X-RAY DIFFRACTION	f_plane_restr	0.0055	1248
X-RAY DIFFRACTION	f_dihedral_angle_d	7.5543	6006

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 (%)
1.6-1.62	0.3861	161	0.3323	3170	X-RAY DIFFRACTION	94.15
1.62-1.64	0.2949	178	0.2873	3387	X-RAY DIFFRACTION	98.84
1.64-1.66	0.29	152	0.2705	3343	X-RAY DIFFRACTION	98.53
1.66-1.68	0.2703	155	0.2631	3368	X-RAY DIFFRACTION	98.41
1.68-1.7	0.3087	186	0.2474	3377	X-RAY DIFFRACTION	98.75
1.7-1.72	0.2555	196	0.235	3261	X-RAY DIFFRACTION	98.41
1.72-1.75	0.2578	206	0.2263	3341	X-RAY DIFFRACTION	98.64
1.75-1.77	0.2498	147	0.213	3420	X-RAY DIFFRACTION	98.37
1.77-1.8	0.219	186	0.2056	3282	X-RAY DIFFRACTION	98.44
1.8-1.83	0.2336	180	0.1995	3347	X-RAY DIFFRACTION	98.3
1.83-1.86	0.2208	190	0.1919	3370	X-RAY DIFFRACTION	98.4
1.86-1.9	0.2396	211	0.1895	3291	X-RAY DIFFRACTION	98.56
1.9-1.93	0.2464	197	0.2073	3289	X-RAY DIFFRACTION	97.54
1.93-1.97	0.2338	179	0.1932	3217	X-RAY DIFFRACTION	95.21
1.97-2.02	0.2119	203	0.1722	3330	X-RAY DIFFRACTION	98.17
2.02-2.06	0.1907	212	0.1672	3343	X-RAY DIFFRACTION	99.22
2.06-2.11	0.2391	178	0.164	3339	X-RAY DIFFRACTION	99.15
2.11-2.17	0.2265	194	0.162	3404	X-RAY DIFFRACTION	99.17
2.17-2.24	0.2133	179	0.1624	3363	X-RAY DIFFRACTION	98.72
2.24-2.31	0.1897	154	0.1608	3414	X-RAY DIFFRACTION	98.51
2.31-2.39	0.1806	168	0.1562	3334	X-RAY DIFFRACTION	98.56
2.39-2.49	0.1886	169	0.1511	3380	X-RAY DIFFRACTION	98.75
2.49-2.6	0.2113	153	0.1557	3369	X-RAY DIFFRACTION	98.19
2.6-2.74	0.1719	146	0.159	3386	X-RAY DIFFRACTION	97.54
2.74-2.91	0.1955	165	0.155	3291	X-RAY DIFFRACTION	96.35
2.91-3.13	0.1565	204	0.1542	3389	X-RAY DIFFRACTION	99.45
3.13-3.45	0.1616	228	0.1399	3366	X-RAY DIFFRACTION	99.45
3.45-3.95	0.1288	140	0.1253	3454	X-RAY DIFFRACTION	99.47
3.95-4.97	0.1397	188	0.1144	3404	X-RAY DIFFRACTION	98.46
4.97-38.98	0.1768	188	0.1532	3462	X-RAY DIFFRACTION	98.38

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	1.88022601473	-0.681323934427	0.245615622627	0.704264498429	-0.0056342708842	0.95340875175	0.00717218470631	-0.223067212822	-0.31284908812	0.0476046592044	0.0927879463537	0.126841798237	0.18008265525	-0.221417663522	-0.0795684220222	0.148925492069	-0.0328124755112	9.20010012646E-5	0.185362268569	0.0480925216446	0.163038993363	-2.87645719768	29.9497656355	24.3115577492
2	4.00201718172	0.279134195935	-0.471209674943	0.912575008196	-0.427756757511	1.91066305587	-0.119018147979	-0.480646407315	-0.0786201848226	0.125458213939	0.178038041071	0.0631096184658	0.144705967713	-0.0459539158517	-0.0368284882335	0.150159289111	0.050576852145	0.00802951409144	0.20615798563	0.0392334612126	0.120371051223	8.6172897002	31.2403941005	35.0890750668
3	3.13226673149	0.269246719633	-1.02939428804	2.34094225602	-2.78552402261	6.22504538493	0.0533198277124	-0.0750680379586	-0.0474838342854	0.0226677802877	-0.0476074546545	-0.123558870566	0.0272710304215	0.473291963171	0.0176049535403	0.134374143786	0.0376555213016	-0.0200046217191	0.119304666828	-0.0306021744984	0.135648556601	23.3346102336	32.7720077894	27.7081475083
4	2.00566508404	-0.172348333024	0.214479234501	2.23627782522	-1.34047018919	3.99065991538	0.0184183915148	-0.076970318613	-0.243954465068	0.0720583106519	-0.00490244183871	-0.0543756408708	0.219161447115	0.276574134916	0.0345910920387	0.146161651938	0.0382641866718	-0.0262219491032	0.107637076921	-0.00710259629344	0.151973985823	19.6351801037	25.5624146205	24.2780484528
5	2.19642490663	-1.42702471171	0.748426684473	2.78200107304	-1.4238341163	1.52387172395	0.0824861357868	0.287424340618	-0.252478282606	-0.166852503848	0.00813162680193	0.121908372026	0.182383824696	-0.0570702989443	-0.0772484878973	0.134501539477	0.00986035557149	-0.00116266585251	0.124354841001	-0.0297274584123	0.138810892983	10.7421532141	29.1750645336	12.4783295016
6	1.81534603953	-0.740683952913	2.0733824777	2.07302516899	-1.1444857338	3.71230435415	0.385445548906	-0.0746744298437	-0.561857424645	0.00146328644782	0.170679962631	0.0225317624291	0.971385462897	0.0451896032637	-0.528090745981	0.236476130353	0.0542229698612	-0.0325602134673	0.253150119305	0.0192550321499	0.337453095378	23.2147826376	17.0145911716	25.6386184816
7	1.58272741645	-1.50745833078	-0.0044606495007	4.55327067848	1.76986816716	3.29849883615	-0.30112338358	-0.369101568007	0.208711164644	0.335915218578	0.161507538952	-0.170830819831	-0.0464226182672	0.0747716698279	0.12372387528	0.196624741815	0.0591266114308	-0.0445956827522	0.215625152095	-0.043072002783	0.141279045346	23.664948548	36.5385690704	38.2937132186
8	1.31517479475	-0.570880255734	-0.520492020568	3.57769823573	0.18263588588	7.04784966243	-0.261020228557	-0.675545602864	-0.156267176734	0.48129986466	0.362173964717	-0.286466249729	-0.0594414861345	0.0730524270126	-0.099932278949	0.306269131977	0.178501408296	-0.0786694560202	0.397456371056	0.0183872016919	0.215740243961	27.6045758862	26.5001075512	45.1097537188
9	3.7379561668	-0.337357378686	0.401977912371	0.476059604367	0.110147706389	0.952791884217	0.0674922502258	0.0979756052065	-0.132482571924	-0.0480227444675	-0.0696908043947	0.0985162093023	0.0491199485221	-0.208775270531	0.00413652317247	0.148733316886	-0.00242576522873	0.00197911423458	0.232612384768	-0.0153139898384	0.126307716099	-22.250893836	42.4412968242	7.97268843109
10	2.16527143814	-0.473204616144	0.313487459939	0.614725152962	-0.0541556724233	0.771921768991	0.00350539562694	0.146762470388	0.249323369652	-0.0282427553163	-0.0291869385653	-0.034055865344	-0.123776319287	-0.0491877534425	0.0218120330915	0.140959959739	0.0264124216613	0.0290399132326	0.1737339178	0.00944959492132	0.138276254657	-11.1048488299	55.7823429748	7.99593133627
11	3.68415292797	-0.464319515833	-1.65924412569	2.29320677885	-0.899209370705	3.86351182956	0.0125394244785	-0.201700273197	0.147585056117	0.111984881785	-0.00985840867779	0.0367805461487	-0.202373838497	-0.0754997635789	-0.0494758587285	0.151038617693	0.0540992056197	-0.0257793542007	0.215917697141	-0.0484352132972	0.178283663851	-28.2005641326	65.6380650754	15.7224283424
12	2.26561493429	0.724896031588	-0.30461940825	3.40355100907	-2.32527579728	3.28641730544	0.000737790620048	-0.115949311467	0.0752942768998	0.0386775026435	0.0233074230537	0.139862140299	-0.0305000452335	-0.239997623441	-0.0636219314808	0.17393606544	0.0643329791878	-0.00826877681715	0.268962106536	-0.0476509667594	0.165490395524	-34.3074897515	59.2125001477	14.7820423299
13	2.5494833161	-1.59014165079	1.51414365297	1.39484535145	-1.27603365761	2.04287454681	0.0208688071049	-0.246266120458	-0.144018499583	0.00181842049905	0.0240184470916	0.0576912638282	-0.00998864005851	-0.252577441889	-0.0648433422065	0.14247353868	0.0173909780739	0.0225311800411	0.370719687974	-0.0290305078377	0.145619127609	-31.0366534237	47.0970012506	18.28718222
14	0.755521079244	0.182447271025	0.928331761654	5.09431484919	-0.663605243258	1.21987500612	-0.0239447717415	0.036237995665	0.0837020839753	-0.453478384911	0.109259220429	0.563187880329	0.0551895698708	-0.190440889398	-0.0945750304376	0.199908800916	0.0807296623815	0.0196015621422	0.397406165676	-0.0463963303442	0.262665553962	-41.9898451444	61.1395920229	7.42956212839
15	8.18289900622	0.210939603003	2.62345333037	3.57579656071	0.196486212721	2.33472663414	-0.0721058546707	-0.268379842768	0.558730226632	0.177151736044	0.0665604211061	-0.34197231702	-0.217371335105	-0.0410317730486	-0.0209912056959	0.283216162003	0.0415167412459	-0.0158324918818	0.23013572867	-0.0672058120873	0.276205024714	-25.1569494467	75.2863318529	17.748659922
16	6.75208481656	1.54461390251	0.164341932781	5.74769816938	-0.397902469972	3.92775349504	-0.0501829067189	-0.0784870535753	0.497147172444	-0.0287104843188	-0.0389335709552	-0.311912225701	-0.485513663255	-0.0163768317274	0.0819683799719	0.30949006092	0.0882157662491	-0.0331794393347	0.224641340032	-0.00194082507675	0.335994667471	-31.5019541106	81.3789069305	8.55347843017

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 13 through 187 )	A	A	13 - 187	13 - 187
2	2	chain 'A' and (resid 188 through 225 )	A	A	188 - 225	188 - 225
3	3	chain 'A' and (resid 226 through 256 )	A	A	226 - 256	226 - 256
4	4	chain 'A' and (resid 257 through 294 )	A	A	257 - 294	257 - 294
5	5	chain 'A' and (resid 295 through 333 )	A	A	333	295
6	6	chain 'A' and (resid 334 through 362 )	A	A	334 - 362	334 - 362
7	7	chain 'A' and (resid 363 through 391 )	A	A	363 - 391	363 - 391
8	8	chain 'A' and (resid 392 through 425 )	A	A	392 - 425	392 - 425
9	9	chain 'B' and (resid 12 through 105 )	B	B	12 - 105	12 - 105
10	10	chain 'B' and (resid 106 through 210 )	B	B	106 - 210	106 - 210
11	11	chain 'B' and (resid 211 through 256 )	B	B	211 - 256	211 - 256
12	12	chain 'B' and (resid 257 through 293 )	B	B	257 - 293	257 - 293
13	13	chain 'B' and (resid 294 through 333 )	B	B	294 - 333	294 - 333
14	14	chain 'B' and (resid 334 through 362 )	B	B	334 - 362	334 - 362
15	15	chain 'B' and (resid 363 through 391 )	B	B	363 - 391	363 - 391
16	16	chain 'B' and (resid 392 through 426 )	B	B	392 - 426	392 - 426

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Protein / Sugars , 2 types, 4 molecules AB

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Non-polymers , 4 types, 836 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi