PDB-7lr6: Crystal structure of GH5_18-E140A from Bifidobacterium longum sub...

ID or keywords:

Entry

Database: PDB / ID: 7lr6

Title

Crystal structure of GH5_18-E140A from Bifidobacterium longum subsp. longum ATCC 55813 in complex with Manb1-4GlcNAc

Components

Glycosyl hydrolase BlGH5_18

Keywords

HYDROLASE / Glycosidase / N-glycan / CAZyme

Function / homology

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

Function and homology information

Biological species

Bifidobacterium longum subsp. longum ATCC 55813 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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	7lr6.cif.gz	818 KB	Display	PDBx/mmCIF format
PDB format	pdb7lr6.ent.gz	561.4 KB	Display	PDB format
PDBx/mmJSON format	7lr6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7lr6_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7lr6_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7lr6_validation.xml.gz	64.7 KB	Display
Data in CIF	7lr6_validation.cif.gz	92.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/7lr6 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/7lr6	HTTPS FTP

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Related structure data

Related structure data	7lqxC 7lr1SC 7lr2C 7lr7C 7lr8C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7lr1-1 7lr2-1 7lr8-d 7lr1-2 6mpc-d 3sae-d 7lr7-1 2xsr-1 3sdr-d 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

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

1

A: Glycosyl hydrolase BlGH5_18

hetero molecules

C: 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

D: 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)	105.257, 142.989, 157.444
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: 49564.191 Da / Num. of mol.: 4 / Mutation: E140A
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: Polysaccharide

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

Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4
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

#3: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO₄

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.99 Å³/Da / Density % sol: 58.84 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 16% PEG 2K, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6

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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: 1.36242 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.36242 Å / Relative weight: 1
Reflection	Resolution: 2.3→39.36 Å / Num. obs: 105883 / % possible obs: 99.9 % / Redundancy: 13 % / B_iso Wilson estimate: 42.62 Å² / CC_1/2: 0.996 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.3→2.34 Å / Num. unique obs: 5206 / CC_1/2: 0.533

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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: 2.3→39.36 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3957 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2059	5139	4.9 %
R_work	0.1609	99789	-
obs	0.1631	104928	99.07 %

Solvent computation

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

Displacement parameters

B_iso mean: 49.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→39.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13231	0	179	685	14095

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0078	13838
X-RAY DIFFRACTION	f_angle_d	0.8861	18928
X-RAY DIFFRACTION	f_chiral_restr	0.0522	2024
X-RAY DIFFRACTION	f_plane_restr	0.0058	2454
X-RAY DIFFRACTION	f_dihedral_angle_d	6.0793	10932

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 (%)
2.3-2.33	0.3264	152	0.3129	3075	X-RAY DIFFRACTION	92.23
2.33-2.35	0.3562	163	0.2705	3329	X-RAY DIFFRACTION	99.54
2.35-2.38	0.3209	178	0.2543	3276	X-RAY DIFFRACTION	99.6
2.38-2.41	0.3147	178	0.2546	3282	X-RAY DIFFRACTION	99.43
2.41-2.44	0.283	165	0.2393	3315	X-RAY DIFFRACTION	99.2
2.44-2.48	0.2749	171	0.2357	3270	X-RAY DIFFRACTION	98.77
2.48-2.51	0.2916	186	0.2246	3242	X-RAY DIFFRACTION	98.28
2.51-2.55	0.3247	161	0.2377	3290	X-RAY DIFFRACTION	98.68
2.55-2.59	0.3541	158	0.2436	3229	X-RAY DIFFRACTION	97.05
2.59-2.63	0.2787	179	0.2251	3321	X-RAY DIFFRACTION	99.23
2.63-2.68	0.3166	137	0.2196	3320	X-RAY DIFFRACTION	98.94
2.68-2.73	0.2678	178	0.1998	3307	X-RAY DIFFRACTION	99.83
2.73-2.78	0.2441	148	0.1961	3332	X-RAY DIFFRACTION	99.49
2.78-2.84	0.2604	194	0.1979	3301	X-RAY DIFFRACTION	99.35
2.84-2.9	0.2614	154	0.205	3305	X-RAY DIFFRACTION	99.08
2.9-2.97	0.2577	155	0.2028	3383	X-RAY DIFFRACTION	99.69
2.97-3.04	0.2924	164	0.1979	3326	X-RAY DIFFRACTION	99.86
3.04-3.12	0.2384	176	0.1921	3327	X-RAY DIFFRACTION	99.63
3.12-3.21	0.2219	175	0.1779	3306	X-RAY DIFFRACTION	98.75
3.21-3.32	0.2341	150	0.1884	3287	X-RAY DIFFRACTION	97.92
3.32-3.44	0.233	185	0.1757	3335	X-RAY DIFFRACTION	99.15
3.44-3.57	0.2379	171	0.1569	3346	X-RAY DIFFRACTION	99.97
3.57-3.74	0.1862	176	0.1373	3354	X-RAY DIFFRACTION	100
3.74-3.93	0.1672	190	0.123	3368	X-RAY DIFFRACTION	99.97
3.93-4.18	0.1464	199	0.1085	3337	X-RAY DIFFRACTION	99.8
4.18-4.5	0.1294	174	0.1049	3378	X-RAY DIFFRACTION	99.8
4.5-4.95	0.1431	175	0.1055	3394	X-RAY DIFFRACTION	99.3
4.95-5.67	0.1491	165	0.1209	3412	X-RAY DIFFRACTION	99.92
5.67-7.13	0.1764	177	0.1475	3468	X-RAY DIFFRACTION	99.95
7.13-39.36	0.165	205	0.1384	3574	X-RAY DIFFRACTION	99.68

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	6.23469724075	2.41726540704	-1.84614282003	4.10807744667	0.841378462757	4.72066364691	0.066191073009	-0.177146934228	0.270746923014	0.205528403733	0.0145681323348	-0.0491099475089	-0.35570507237	0.126854377124	-0.0646876109499	0.221937162879	0.0624231661083	-0.0355752240556	0.301747363561	-0.0325624373048	0.246597480481	53.2308597372	6.99758360246	-10.4938118706
2	1.50981167738	0.0796943405874	-1.12730528812	0.452576781179	0.0580524301113	1.99945896645	-0.0181021978227	-0.0583998408675	-0.0686244216184	0.0204449816158	-0.0977026104699	0.00297562455555	-0.0377289875532	-0.00144711796193	0.0503269016796	0.290653538952	0.00783396688516	-0.00252323372433	0.327974255975	0.0137999376529	0.289610299774	62.7574905566	0.704461742418	-19.8586913671
3	1.44880628837	0.0812482657191	-1.13606544275	1.23143224033	0.601242677764	4.48629228775	-0.132069920886	-0.252600450505	-0.167940250258	0.0246248927059	0.0316926431641	-0.0866176413932	0.153260705244	0.221461757267	0.160056497436	0.340316566947	0.00641117083392	0.00502572044914	0.333403966453	0.0369146639208	0.357326408882	65.368143396	-6.65947206056	-17.8616186748
4	2.22725485053	-0.188360167765	-1.30277652143	3.20946610053	0.0948656706284	2.26461708552	-0.0832543736519	0.216376044091	-0.376662415309	-0.479684871172	-0.00950768853528	0.0805627847481	0.497149214067	-0.0530098229987	0.217849320911	0.390191142141	-0.0279917172113	0.050753863557	0.335061059389	-0.0381826125314	0.406261713778	60.6884321093	-12.9388280975	-30.677804502
5	1.5245171027	0.361749125029	-0.628780058365	2.27924712228	-0.123391966406	1.02722927846	-0.0283268392932	0.179330488498	-0.041762081373	-0.0731975431944	-0.0796258966926	0.140572960352	0.0752898614595	-0.179728113753	0.0627413376209	0.286790454087	-0.0216601805554	-0.0128673896758	0.399257257689	-0.0535452391455	0.290860039358	43.8006075422	-8.84911871673	-19.8335276906
6	1.38698481543	0.901814635916	-0.316572668634	2.88515044364	0.574099323216	2.20525915278	0.161326464235	-0.129930614525	0.203031087863	0.510076838876	-0.106554024943	0.243448395489	-0.190789084473	-0.121490862265	0.0396635144181	0.246459303737	0.0214641049192	0.000267995284431	0.390064475085	-0.0742441292563	0.355589005487	39.4776673696	-0.589856281675	-10.3039283595
7	1.84885583555	0.593566573591	0.223397903434	3.08234778033	-0.430608646243	1.19109988181	-0.0250589505988	0.222247580273	-0.169469664289	-0.348954836043	-0.0213266698501	0.109275486103	0.307742033672	-0.213534714548	0.0723533315374	0.453674783892	-0.0851633560185	-0.0244186873684	0.500252911173	-0.12970688348	0.439219802694	37.9866128159	-22.3367680769	-26.8310011953
8	6.7505183894	-0.465591692619	-0.358343461122	1.60439490713	-1.31223015001	3.09312108167	0.00351535085328	0.145765472549	0.27062480274	-0.0335437806287	0.0643217466427	0.197312260048	-0.227599979496	-0.212309024366	-0.128854763566	0.396232699349	-0.0745420826803	-0.0433196838505	0.356988228133	-0.0145922197575	0.33432088491	-8.21564712227	20.019916939	-8.7786050729
9	1.45074011627	0.232391914173	-0.86497650272	0.61953639208	-0.490067774689	2.52792304353	-0.10855779005	-0.0151086076953	-0.064240746181	-0.0883456684216	0.0220147127949	-0.000145461403364	0.0102092192163	-0.0503877110792	0.0847759112519	0.310835283457	-0.0108181839623	-0.0118094110275	0.361474166077	-0.0489591259933	0.332250561905	-12.1605641782	7.18353406537	0.128414612511
10	3.80225849119	0.190839187656	-0.359615358905	6.5890984347	-0.075844562195	2.59873675189	-0.19036539184	-0.628965896063	-0.0639397255502	0.435005998206	0.0926536045381	-0.518459228445	0.120433884067	0.600570132666	0.0996237867211	0.291199893707	0.0494151013676	0.00998942828956	0.506790210409	-0.012111754598	0.38821172092	-3.20965935096	-0.104353534683	13.7782581341
11	2.00459822386	-0.198582205049	-0.281818461239	0.817374353529	-0.506191721991	1.02673082025	-0.0847492854351	-0.143200103024	0.144515615684	-0.0250318199037	0.0499332336826	-0.201196026494	-0.133149703279	0.353766915046	0.0280769693183	0.319061887785	-0.0652858281753	-0.0045067965485	0.504976569899	-0.0590382491201	0.365191961289	8.06542294813	11.4110437297	0.868909442787
12	3.96418545604	-2.33344847858	1.48733944293	2.95602282899	-1.12067114993	2.93617340445	0.251613379329	0.532637803714	0.483117797577	-0.429851040528	-0.275067971191	-0.150884528175	-0.419126649152	0.376457860329	-0.0496266262849	0.371043326256	-0.171919946839	-0.00053609833517	0.491114645219	0.0194566020352	0.450161514796	7.88143218717	20.8761489337	-8.63742695528
13	2.40941465176	-0.405706504421	-0.365541634096	2.29744584798	0.709705647717	1.55739564874	-0.237943375336	-0.416722750808	-0.11340906578	0.0187042756644	0.243537936544	-0.205621918814	-0.0493239069923	0.510968648463	-0.00660386040601	0.311513644687	-0.00208754157675	0.00642209183146	0.743830195435	-0.0320455291684	0.37627323176	20.483020996	3.43723316379	8.04722509631
14	5.12094113098	-1.6543394637	-0.371964618375	1.85234849754	-0.498240582222	3.2963454111	0.113988039809	0.693328058326	-0.141162720742	-0.330983578242	-0.1960568423	0.203537038571	-0.075070565816	-0.139533877587	-0.0870028701331	0.285578988855	0.0219374728076	-0.0223503085852	0.362281443303	-0.0111012472696	0.301813107898	22.6808170325	-52.043274225	-53.1981412669
15	1.5325595321	-0.478095804119	-0.0511644203415	0.860291204345	0.127150647356	1.1461701444	0.0528401278231	-0.122220703183	0.231162005086	-0.00972706212729	-0.00803239515787	-0.125373364432	-0.165709526947	0.0954880318554	-0.0298253841211	0.325031398476	-0.0563078610361	0.00125667676143	0.319974881177	-0.0148906585007	0.331619062287	38.3007792123	-51.4413614376	-44.0085867061
16	0.967526822051	0.253551101861	-0.0424550241774	0.993956297673	0.475827844832	1.7429774374	0.0437883290374	0.0215041908699	0.109823856188	0.00553506691598	-0.0517596954864	0.0463332406615	-0.24425747482	-0.0913058002527	-0.0013334983053	0.316534446329	-0.000721823188594	0.0126075981443	0.301164319243	-0.0298162245721	0.302734560024	20.3555684933	-51.4215678574	-31.4636692352
17	2.84913219755	0.0392172481575	-0.143666320885	6.70204967831	0.938347917404	2.26514076677	0.157304933806	-0.211377788506	0.194431885503	0.345795423208	-0.103598478409	-0.110156941128	-0.0355415115977	-0.166445388596	-0.0493465254047	0.34932794571	-0.0480119189012	-0.00792710234438	0.412595352938	-0.0345131825226	0.297267381374	22.1959121561	-48.5561039939	-16.1016172128
18	3.61965487028	0.47724127655	-0.145007379045	0.505445083148	0.349201153899	1.23451829401	-0.00993871222935	0.0181835680898	-0.274537399245	-0.00791401293146	0.0592318562797	0.00603366109058	0.189512633994	-0.0555030378344	-0.0335973590846	0.393235640579	0.0164030408176	0.0212158503946	0.288060871526	0.0808236304903	0.37024127409	-21.948719574	-21.0180923352	-68.5949105225
19	0.696438955096	0.0922878179504	-0.0192917048296	0.770590520459	-0.121327745125	1.13670093331	-0.0381035880977	-0.186711411491	-0.223610855014	0.0781650697246	0.0589671911721	-0.012420302612	0.272519035873	0.137788959918	-0.0281984167045	0.396064628233	0.0796424740639	0.00664599558989	0.42062310716	0.100597609282	0.401573162478	-13.229314843	-16.0143937376	-51.5628396937
20	3.89189540204	-0.0335119534255	-1.32029791023	4.9731300286	1.62878716316	2.16375948296	-0.235060756875	-0.323653525968	-0.351989203287	0.460755499837	0.247119119893	-0.0404613553256	0.311586361599	0.177375133739	-0.0191132330351	0.420251465933	0.089138989771	0.0162090477573	0.488872485497	0.136480873549	0.312409364624	-10.7306963604	-17.8520399786	-35.5459299899

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 0 through 34 )	A	A	0 - 34	0 - 34
2	2	chain 'A' and (resid 35 through 108 )	A	A	35 - 108	35 - 108
3	3	chain 'A' and (resid 109 through 145 )	A	A	109 - 145	109 - 145
4	4	chain 'A' and (resid 146 through 171 )	A	A	146 - 171	146 - 171
5	5	chain 'A' and (resid 172 through 302 )	A	A	172 - 302	172 - 302
6	6	chain 'A' and (resid 303 through 341 )	A	A	303 - 341	303 - 341
7	7	chain 'A' and (resid 342 through 423 )	A	A	342 - 423	342 - 423
8	8	chain 'B' and (resid 0 through 34 )	B	B	0 - 34	0 - 34
9	9	chain 'B' and (resid 35 through 145 )	B	B	35 - 145	35 - 145
10	10	chain 'B' and (resid 146 through 167 )	B	B	146 - 167	146 - 167
11	11	chain 'B' and (resid 168 through 302 )	B	B	168 - 302	168 - 302
12	12	chain 'B' and (resid 303 through 341 )	B	B	303 - 341	303 - 341
13	13	chain 'B' and (resid 342 through 423 )	B	B	342 - 423	342 - 423
14	14	chain 'C' and (resid 0 through 34 )	C	C	0 - 34	0 - 34
15	15	chain 'C' and (resid 35 through 171 )	C	C	35 - 171	35 - 171
16	16	chain 'C' and (resid 172 through 375 )	C	C	172 - 375	172 - 375
17	17	chain 'C' and (resid 376 through 422 )	C	C	376 - 422	376 - 422
18	18	chain 'D' and (resid 0 through 128 )	D	D	0 - 128	0 - 128
19	19	chain 'D' and (resid 129 through 375 )	D	D	129 - 375	129 - 375
20	20	chain 'D' and (resid 376 through 422 )	D	D	376 - 422	376 - 422

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