PDB-8rg5: Crystal structure of PbFucA from Planctomycetes bacterium K23_9 i...

ID or keywords:

Entry

Database: PDB / ID: 8rg5

Title

Crystal structure of PbFucA from Planctomycetes bacterium K23_9 in P 4 21 2

Components

Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein

Keywords

HYDROLASE / Fucoidan / endo-fucoidanase / endo-fucanase / GH168 / glycosyl hydrolase

Function / homology

Hypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein

Function and homology information

Biological species

Planctomycetes bacterium K23_9 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

Perez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Lorizate, M. / Arrizabalaga, U. / Garcia-Alija, M. / Terrones, O. / Contreras, F.X. / Guerin, M.E. / Trastoy, B. / Alonso-Saez, L.

Funding support

Spain, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota.
Authors: Perez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Terrones, O. / Arrizabalaga, U. / Garcia-Alija, M. / Lorizate, M. / Martinez Gascuena, A. / Garcia-Alvarez, I. / Nieto-Garai, J.A. / ...

History

Deposition	Dec 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 1, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8rg5.cif.gz	407.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8rg5.ent.gz	339.8 KB	Display	PDB format
PDBx/mmJSON format	8rg5.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/rg/8rg5 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/8rg5	HTTPS FTP

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Related structure data

Related structure data	8rg3C 8rg4C 9f9vC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein

B: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein

hetero molecules

82.9 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)	139.295, 139.295, 104.686
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein Mass: 41066.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planctomycetes bacterium K23_9 (bacteria) Gene: K239x_02140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A517NMB4
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Microseeding of PbFucA-1 Molecular Dimensions (0.12 M alcohols, 0.1 M buffer system 3 pH 8.5, 30% v/v precipitant mix 2)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.18→29.85 Å / Num. obs: 54279 / % possible obs: 99.93 % / Redundancy: 27 % / B_iso Wilson estimate: 30.94 Å² / CC_1/2: 0.9 / R_merge(I) obs: 0.15 / R_rim(I) all: 0.15 / Net I/σ(I): 20.91
Reflection shell	Resolution: 2.18→2.26 Å / Num. unique obs: 5322 / CC_1/2: 0.96

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.18→29.85 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2446	2648	4.88 %
R_work	0.2032	-	-
obs	0.2052	54279	99.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.18→29.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5572	0	52	141	5765

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	579
X-RAY DIFFRACTION	f_angle_d	0.975	781
X-RAY DIFFRACTION	f_dihedral_angle_d	6.767	783
X-RAY DIFFRACTION	f_chiral_restr	0.055	801
X-RAY DIFFRACTION	f_plane_restr	0.008	1011

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 (%)
2.18-2.22	0.2621	118	0.2063	2566	X-RAY DIFFRACTION	96
2.22-2.26	0.212	152	0.201	2674	X-RAY DIFFRACTION	100
2.26-2.3	0.2331	125	0.1984	2681	X-RAY DIFFRACTION	100
2.3-2.35	0.2554	146	0.2078	2687	X-RAY DIFFRACTION	100
2.35-2.41	0.2627	143	0.2026	2673	X-RAY DIFFRACTION	100
2.41-2.47	0.253	131	0.1969	2699	X-RAY DIFFRACTION	100
2.47-2.54	0.261	150	0.2007	2686	X-RAY DIFFRACTION	100
2.54-2.61	0.2911	130	0.203	2705	X-RAY DIFFRACTION	100
2.61-2.7	0.2532	145	0.1971	2688	X-RAY DIFFRACTION	100
2.7-2.79	0.2787	143	0.2002	2698	X-RAY DIFFRACTION	100
2.79-2.9	0.2576	120	0.1977	2738	X-RAY DIFFRACTION	100
2.9-3.03	0.2312	156	0.1985	2678	X-RAY DIFFRACTION	100
3.04-3.19	0.2403	132	0.1954	2714	X-RAY DIFFRACTION	100
3.19-3.39	0.2258	131	0.1947	2752	X-RAY DIFFRACTION	100
3.39-3.66	0.2521	129	0.2003	2750	X-RAY DIFFRACTION	100
3.66-4.02	0.2201	148	0.1898	2736	X-RAY DIFFRACTION	100
4.02-4.6	0.2421	131	0.1958	2777	X-RAY DIFFRACTION	100
4.6-5.79	0.2519	155	0.2122	2801	X-RAY DIFFRACTION	100
5.79-29.85	0.2405	163	0.2391	2928	X-RAY DIFFRACTION	100

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	3.6108	-0.1177	1.7004	3.2881	1.3477	2.972	-0.0559	0.1882	0.0698	-0.1046	0.0704	-0.142	-0.1947	0.1782	-0.046	0.2031	0.0107	0.0258	0.1555	0.0021	0.1773	53.4911	6.1374	7.7691
2	1.4514	-0.2582	0.7077	1.4322	1.8179	5.6784	-0.1892	-0.1314	-0.0121	0.1721	0.1413	-0.1933	-0.1881	0.0878	0.0458	0.2727	0.0337	-0.0694	0.1883	0.0225	0.3088	60.2033	12.7488	26.8527
3	1.5108	-0.1657	0.4405	0.9898	0.8156	1.8531	-0.2814	-0.108	0.2639	0.0446	0.1596	-0.1039	-0.5247	-0.0753	0.1062	0.3975	0.0754	-0.109	0.1968	-0.004	0.2827	52.7211	22.6666	25.654
4	3.6673	1.2248	-0.0856	2.0576	0.2485	2.3767	-0.1537	-0.0305	0.2807	0.0714	0.0209	0.0874	-0.4497	-0.2235	0.1952	0.3317	0.1101	-0.0586	0.282	-0.0229	0.2679	41.5739	17.632	19.5102
5	2.5299	-0.5234	0.4882	3.4481	0.9284	1.6387	-0.1187	-0.1003	-0.0516	0.3105	0.0274	0.1432	-0.1576	-0.4087	0.089	0.255	0.0628	-0.008	0.3268	-0.0268	0.1856	38.0675	6.8365	13.9761
6	3.7225	-1.7062	1.441	7.6314	-1.8731	4.1402	0.0179	0.1565	-0.224	-0.1428	-0.0006	-0.0187	-0.0153	0.0316	0.0339	0.1066	-0.0316	0.0325	0.1707	-0.0414	0.1705	42.9352	3.3841	7.5059
7	6.1749	-1.6307	-5.7721	2.2105	1.3347	6.8361	0.0043	0.3853	-0.0063	-0.1314	-0.2146	0.3471	-0.1913	-1.0164	0.1696	0.2479	0.089	-0.0721	0.4205	-0.0592	0.2903	27.1712	9.2002	4.959
8	4.4419	2.0038	1.0514	3.0335	0.1486	1.5964	0.1476	-0.1856	-0.269	-0.0902	0.0639	-0.0397	0.4539	-0.153	-0.1974	0.3106	-0.0696	-0.0366	0.2193	0.0216	0.2043	48.5124	-34.4424	4.0973
9	2.4721	0.5329	1.501	0.4243	-0.063	1.7835	-0.0361	0.1711	-0.0854	-0.4523	0.3667	0.346	0.4595	-0.3099	-0.1942	0.4926	-0.2124	-0.1184	0.3837	0.0689	0.3397	37.8851	-39.342	-2.531
10	0.0325	-0.0479	0.1198	0.0825	-0.1953	0.4855	-0.2396	0.2302	0.321	-0.4544	0.2272	0.4058	0.0413	-0.1248	-0.1987	0.6075	-0.4053	-0.3367	0.5307	0.2142	0.56	32.8992	-25.2032	-12.1094
11	0.8513	-0.8854	0.8286	0.9483	-0.7119	1.8809	-0.373	0.2318	0.4059	-0.5072	0.4337	0.3626	0.1909	-0.353	-0.1336	0.4364	-0.236	-0.1958	0.3775	0.122	0.4196	38.7057	-19.0619	-10.4
12	0.7284	-0.0443	0.207	0.5176	-0.4916	1.7467	-0.2312	-0.0757	0.5482	-0.3305	0.2179	0.5444	-0.181	-0.2476	0.0358	0.3692	-0.1623	-0.2831	0.5121	0.1516	0.8221	32.4055	-12.3332	-8.55
13	3.8242	0.7742	0.512	2.0545	-0.4836	1.8557	-0.0739	0.0687	0.3272	-0.1701	0.1302	0.2687	0.094	-0.1904	-0.0018	0.2443	-0.0376	-0.0361	0.2168	0.0013	0.2644	50.4298	-15.1278	-3.7568
14	3.29	-0.2148	0.4026	2.8748	0.5889	2.3651	-0.0778	0.3051	-0.2808	-0.3338	0.0372	0.0541	0.3937	0.108	0.0138	0.3121	-0.0316	0.0112	0.187	-0.0362	0.2143	59.2974	-27.8245	-4.1672
15	3.6171	2.4243	1.953	7.1193	2.6465	4.8062	0.0051	0.0869	-0.3363	-0.2392	0.1037	-0.0886	0.4872	-0.136	-0.0677	0.1687	0.007	0.0452	0.1931	-0.0106	0.2212	58.5659	-30.8169	2.5484
16	4.2685	3.7624	-6.2173	5.2779	-5.744	9.2332	-0.0074	-0.27	-0.1038	0.1721	-0.2052	-0.2756	-0.0317	0.6786	0.201	0.1742	0.0041	-0.0505	0.2327	-0.0705	0.2317	69.2972	-17.8848	5.1789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 39 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 through 239 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 240 through 263 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 264 through 335 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 336 through 362 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 363 through 392 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 39 through 78 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 104 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 105 through 173 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 174 through 199 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 200 through 221 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 222 through 279 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 280 through 335 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 336 through 362 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 363 through 392 )

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