PDB-8tdh: Structure of trehalose bound Alistipes sp. Glucoside-3-dehydrogen...

ID or keywords:

Entry

Database: PDB / ID: 8tdh

Title

Structure of trehalose bound Alistipes sp. Glucoside-3-dehydrogenase AL3

Components

Predicted dehydrogenases and related proteins

Keywords

OXIDOREDUCTASE / dehydrogenase

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Alistipes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

Lazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J.

Funding support

Canada, 1items

Citation

Journal: Nature / Year: 2024
Title: An alternative broad-specificity pathway for glycan breakdown in bacteria.
Authors: Nasseri, S.A. / Lazarski, A.C. / Lemmer, I.L. / Zhang, C.Y. / Brencher, E. / Chen, H.M. / Sim, L. / Panwar, D. / Betschart, L. / Worrall, L.J. / Brumer, H. / Strynadka, N.C.J. / Withers, S.G.

History

Deposition	Jul 3, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2024	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jul 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8tdh.cif.gz	868 KB	Display	PDBx/mmCIF format
PDB format	pdb8tdh.ent.gz	609 KB	Display	PDB format
PDBx/mmJSON format	8tdh.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8tdh_validation.pdf.gz	8.1 MB	Display	wwPDB validaton report
Full document	8tdh_full_validation.pdf.gz	8.2 MB	Display
Data in XML	8tdh_validation.xml.gz	70.9 KB	Display
Data in CIF	8tdh_validation.cif.gz	94.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/td/8tdh ftp://data.pdbj.org/pub/pdb/validation_reports/td/8tdh	HTTPS FTP

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Related structure data

Related structure data	8tcdC 8tcrC 8tcsC 8tctC 8tdaC 8tdeC 8tdfC 8tdiC 8v31 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
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (1) #111 - Mar 2009 Hydrogenase similarity (1)

Deposited unit

A: Predicted dehydrogenases and related proteins

B: Predicted dehydrogenases and related proteins

C: Predicted dehydrogenases and related proteins

D: Predicted dehydrogenases and related proteins

hetero molecules

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

1

A: Predicted dehydrogenases and related proteins

B: Predicted dehydrogenases and related proteins

hetero molecules

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

2

C: Predicted dehydrogenases and related proteins

D: Predicted dehydrogenases and related proteins

hetero molecules

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

Unit cell

Length a, b, c (Å)	186.581, 57.221, 224.962
Angle α, β, γ (deg.)	90, 106.584, 90
Int Tables number	5
Space group name H-M	I121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 40 - 490 / Label seq-ID: 1 - 451

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein

Predicted dehydrogenases and related proteins

Mass: 50593.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Alistipes (bacteria) / Gene: BN590_01570 / Production host:

Escherichia coli (E. coli) / References: UniProt: R6XLM3

#2: Polysaccharide

alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose

#3: Polysaccharide

alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose

#4: Chemical

ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Mass: 663.425 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.74 Å³/Da / Density % sol: 55.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M Sodium Malonate 17% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.95→162.27 Å / Num. obs: 43707 / % possible obs: 89.9 % / Redundancy: 2.7 % / CC_1/2: 0.95 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.141 / R_rim(I) all: 0.199 / Net I/σ(I): 3.5
Reflection shell	Resolution: 2.95→3.06 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.462 / Num. unique obs: 3079 / CC_1/2: 0.497 / R_pim(I) all: 0.462 / R_rim(I) all: 0.654

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.95→162.267 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.848 / WR_factor R_free: 0.266 / WR_factor R_work: 0.214 / SU B: 50.816 / SU ML: 0.424 / Average fsc free: 0.9566 / Average fsc work: 0.9725 / Cross valid method: THROUGHOUT / ESU R Free: 0.462
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2471	2195	5.022 %	RANDOM
R_work	0.1949	41511	-	-
all	0.198	-	-	-
obs	-	43706	89.655 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 40.815 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.91 Å²	-0 Å²	1.823 Å²
2-	-	-1.193 Å²	-0 Å²
3-	-	-	3.412 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→162.267 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14208	0	682	118	15008

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	15324
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	13962
X-RAY DIFFRACTION	r_angle_refined_deg	5.641	1.847	20951
X-RAY DIFFRACTION	r_angle_other_deg	0.682	1.766	32353
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.848	5	1800
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.348	5	95
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.947	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.604	10	2379
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.774	10	665
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2369
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	17549
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3415
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	3123
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	13425
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	7548
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	8004
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.194	0.2	288
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.03	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.208	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.436	0.392	7212
X-RAY DIFFRACTION	r_mcbond_other	0.436	0.392	7212
X-RAY DIFFRACTION	r_mcangle_it	0.789	0.702	9008
X-RAY DIFFRACTION	r_mcangle_other	0.789	0.703	9009
X-RAY DIFFRACTION	r_scbond_it	1.428	0.655	8112
X-RAY DIFFRACTION	r_scbond_other	1.428	0.656	8113
X-RAY DIFFRACTION	r_scangle_it	2.453	1.178	11916
X-RAY DIFFRACTION	r_scangle_other	2.453	1.179	11917
X-RAY DIFFRACTION	r_lrange_it	3.573	4.354	16740
X-RAY DIFFRACTION	r_lrange_other	3.562	4.353	16740
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.074	0.05	14521
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.073	0.05	14500
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.075	0.05	14449
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.075	0.05	14518
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.075	0.05	14526
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	14497

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07412	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07412	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07335	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07335	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07524	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07524	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0746	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0746	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07462	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07462	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07101	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07101	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.95-3.027	0.338	118	0.285	2161	0.288	3554	0.925	0.948	64.1249	0.287
3.027-3.11	0.304	126	0.265	2191	0.267	3478	0.939	0.957	66.6187	0.265
3.11-3.2	0.33	112	0.255	2328	0.258	3374	0.929	0.958	72.3177	0.257
3.2-3.298	0.288	120	0.245	2580	0.247	3256	0.949	0.963	82.9238	0.245
3.298-3.406	0.256	141	0.247	2817	0.247	3224	0.952	0.961	91.7494	0.245
3.406-3.526	0.286	157	0.236	2853	0.239	3110	0.939	0.965	96.7846	0.236
3.526-3.659	0.27	162	0.208	2750	0.211	2949	0.955	0.974	98.7453	0.21
3.659-3.808	0.225	121	0.188	2728	0.189	2904	0.967	0.979	98.1061	0.191
3.808-3.977	0.242	160	0.184	2538	0.188	2759	0.962	0.978	97.7891	0.189
3.977-4.171	0.218	127	0.167	2392	0.17	2604	0.97	0.981	96.7358	0.175
4.171-4.397	0.219	135	0.15	2350	0.154	2556	0.97	0.985	97.2222	0.163
4.397-4.663	0.21	120	0.137	2181	0.141	2366	0.976	0.987	97.2527	0.153
4.663-4.985	0.208	106	0.146	2064	0.149	2230	0.978	0.985	97.3094	0.156
4.985-5.384	0.243	111	0.163	1931	0.167	2105	0.963	0.984	97.0071	0.176
5.384-5.897	0.225	75	0.171	1839	0.173	1952	0.967	0.981	98.0533	0.185
5.897-6.592	0.243	81	0.167	1632	0.17	1751	0.959	0.983	97.8298	0.182
6.592-7.61	0.221	83	0.173	1422	0.176	1559	0.965	0.979	96.5362	0.196
7.61-9.315	0.197	58	0.174	1244	0.175	1345	0.968	0.982	96.803	0.193
9.315-13.152	0.244	55	0.217	947	0.219	1043	0.971	0.976	96.069	0.24
13.152-162.267	0.316	27	0.349	563	0.347	630	0.944	0.933	93.6508	0.759

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	0.7984	-0.0511	-0.1655	0.9213	-0.2433	1.002	-0.0211	-0.0042	0.0301	-0.0109	0.0088	-0.0111	0.0267	-0.1197	0.0123	0.4914	0.0277	-0.0721	0.1831	-0.0178	0.0128	26.3397	-2.142	32.4859
2	1.2483	-0.3562	0.3291	0.8712	-0.0076	1.1054	-0.0176	0.0048	0.1921	-0.0656	-0.0863	-0.2784	0.0248	0.3011	0.1038	0.4931	0.0581	0.0192	0.3146	0.0488	0.2095	68.1785	-5.971	31.8049
3	1.7116	-0.1156	0.15	0.8875	-0.2585	0.9706	-0.2092	0.5253	0.2545	-0.0613	0.0816	-0.0593	-0.052	-0.2073	0.1276	0.5718	-0.1587	-0.1096	0.5409	0.0933	0.1107	27.785	-30.4298	-22.629
4	1.7808	0.2014	-0.6189	0.7937	0.0749	0.9063	-0.3181	0.3896	-0.1582	-0.1324	0.0313	-0.2807	0.165	0.0574	0.2867	0.6239	-0.1473	0.0045	0.5692	0.1006	0.2747	68.251	-41.2857	-26.8076

Refinement TLS group

Selection: ALL

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