PDB-7shg: Polysaccharide ribofuranosyl transferase from Thermobacillus composti

ID or keywords:

Entry

Database: PDB / ID: 7shg

Title

Polysaccharide ribofuranosyl transferase from Thermobacillus composti

Components

Ribofuranosyl transferase

Keywords

TRANSFERASE / glycosyltransferase / phosphatase / ribofuranose

Function / homology

haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / metal ion binding / Haloacid dehalogenase superfamily enzyme, subfamily IA

Function and homology information

Biological species

Thermobacillus composti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Kimber, M.S. / Kelly, S.D.

Funding support

Canada, 1items

Citation

Journal: Nat.Chem.Biol. / Year: 2022
Title: The biosynthetic origin of ribofuranose in bacterial polysaccharides.
Authors: Kelly, S.D. / Williams, D.M. / Nothof, J.T. / Kim, T. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.

History

Deposition	Oct 8, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7shg.cif.gz	601.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7shg.ent.gz	417.9 KB	Display	PDB format
PDBx/mmJSON format	7shg.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/sh/7shg ftp://data.pdbj.org/pub/pdb/validation_reports/sh/7shg	HTTPS FTP

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Related structure data

Similar structure data	3kta-d 7shg-2 7jmo-d 7chb-d 3txv-2 7b3o-d 5k1s-2 2xny-2 4pxb-d 1re4-2 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 - 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	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Ribofuranosyl transferase

B: Ribofuranosyl transferase

hetero molecules

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

1

A: Ribofuranosyl transferase

hetero molecules

defined by author&software
Evidence: assay for oligomerization, Monomeric based on SEC-MALS experiments
76.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ribofuranosyl transferase

hetero molecules

defined by author&software
76.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.740, 82.500, 234.920
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-856- HOH

#1: Protein	Ribofuranosyl transferase Mass: 76409.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobacillus composti (bacteria) / Strain: DSM 18247 / JCM 13945 / KWC4 / Gene: Theco_3912 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: L0EJI9
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.27 Å³/Da / Density % sol: 45.92 % / Description: plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10 mM MgCl2, 10% PEG 20000, 100 mM Na HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9811 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9811 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 83914 / % possible obs: 90 % / Redundancy: 4.93 % / B_iso Wilson estimate: 48.18 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.133 / Net I/σ(I): 6.22
Reflection shell	Resolution: 2.5→2.6 Å / R_merge(I) obs: 1.153 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 9187 / CC_1/2: 0.675 / % possible all: 88.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.5→49.16 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.5089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2949	2154	2.58 %
R_work	0.2511	81298	-
obs	0.2522	83452	89.56 %

Solvent computation

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

Displacement parameters

B_iso mean: 62.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→49.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9835	0	5	177	10017

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	10056
X-RAY DIFFRACTION	f_angle_d	0.4874	13550
X-RAY DIFFRACTION	f_chiral_restr	0.0406	1467
X-RAY DIFFRACTION	f_plane_restr	0.0034	1724
X-RAY DIFFRACTION	f_dihedral_angle_d	14.6644	3757

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 (%)
2.5-2.56	0.3986	147	0.3878	5366	X-RAY DIFFRACTION	88.6
2.56-2.62	0.3525	142	0.3788	5315	X-RAY DIFFRACTION	88.42
2.62-2.69	0.3087	143	0.3539	5353	X-RAY DIFFRACTION	88.53
2.69-2.77	0.3826	143	0.3499	5446	X-RAY DIFFRACTION	89.75
2.77-2.86	0.3659	148	0.3264	5540	X-RAY DIFFRACTION	91.12
2.86-2.96	0.3627	150	0.3294	5542	X-RAY DIFFRACTION	91.36
2.96-3.08	0.4135	147	0.318	5444	X-RAY DIFFRACTION	90.75
3.08-3.22	0.3447	145	0.3025	5501	X-RAY DIFFRACTION	90.82
3.22-3.39	0.3275	141	0.2635	5443	X-RAY DIFFRACTION	89.92
3.39-3.61	0.2966	139	0.2511	5482	X-RAY DIFFRACTION	90.25
3.61-3.88	0.3005	147	0.2329	5407	X-RAY DIFFRACTION	89.74
3.88-4.27	0.277	144	0.2202	5371	X-RAY DIFFRACTION	88.82
4.27-4.89	0.2514	139	0.1903	5373	X-RAY DIFFRACTION	88.69
4.89-6.16	0.2461	142	0.2205	5381	X-RAY DIFFRACTION	88.87
6.16-49.16	0.2418	137	0.1883	5334	X-RAY DIFFRACTION	87.86

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	3.18259246602	0.286966191859	0.201274691748	0.298701665536	-0.754432808541	2.10568054157	0.04381568409	0.180478996251	0.107202890338	-0.060776350726	-0.121704804541	-0.00784474842039	-0.489180446922	-0.786577334884	9.92171611729E-5	0.542119088535	-0.140099628389	-0.0312880380416	0.722038152906	0.0543779139712	0.501801288214	49.448	68.305	23.207
2	1.43309306854	0.267551441888	-0.352875777797	0.63573034511	0.220783434998	0.489925756606	-0.214182499204	0.243130740038	0.432724158982	-0.0801757687301	-0.0459751222851	0.0138329286144	-1.16790376094	-0.240205265877	-8.65871282977E-5	1.05286009551	-0.102981238456	-0.084250628719	1.02780221461	-0.0137030916365	0.689515939544	53.838	82.456	24.568
3	2.71047746737	0.560130886127	-0.284433284543	0.876343343534	-1.33428641354	2.54356624324	-0.184762890594	0.276551994367	-0.187468774907	-0.0425119920095	0.0678642459009	-0.177441510979	0.567849098297	-0.609440022886	6.97220472723E-5	0.517913897714	-0.140530775625	-0.0196776837253	0.678035434902	-0.0102236630662	0.537043326365	58.098	59.552	13.022
4	1.14285530478	0.543012174112	-1.29903992109	1.65220055837	-0.481369396551	1.48847670679	-0.102155185593	0.281776963001	0.113456698725	-0.0733755644963	-0.0769611060983	-0.132398834184	-0.101228143043	-0.375696440608	-5.07452615964	0.552969437752	-0.0894653516934	-0.0497245338675	0.781083848268	0.0338520473425	0.51233492162	56.626	67.263	4.921
5	0.830105839113	0.689507798217	-1.2113604953	0.639309807778	-1.07077017194	1.71276492034	-0.342259319539	0.596204109305	0.150052160301	-0.0114269166817	0.427260820216	0.047856807272	0.439929670317	-0.886464644119	-0.000256550612494	0.54015855053	-0.20412530597	-0.0110581179793	0.842257505346	-0.0475058660559	0.566232346098	40.389	59.191	19.822
6	2.67324886064	0.88472100914	0.730296635989	0.723613126288	1.12372290353	1.94304871522	0.0175246734632	-0.0703530529177	-0.088178796132	-0.00225264920078	-0.107725076643	0.110061607804	0.00573649658109	-0.220964773319	-2.87672921357	0.517924817174	-0.109395284674	-0.00909095198592	0.756582801547	0.0148921526821	0.521287279665	53.507	56.535	48.838
7	1.4326936826	-0.0782619799506	1.26477462561	0.238320949487	0.227045014117	1.28573442043	-0.148424613287	-0.133836497023	0.0503233093781	0.211450553732	-0.0467779734146	0.0747352533324	0.104114622502	0.280147976767	-4.07285647828E-5	0.605542032351	-0.14336046651	-0.00293141695699	0.783814408654	0.0429368294276	0.523467391927	64.249	61.134	63.896
8	1.31904045286	0.188966980807	-0.0156629799188	2.20628848391	0.295145497356	1.23782543762	0.0580442547533	0.138509235881	-0.273355432476	0.586358775588	-0.201915882352	-0.0918821413987	0.530550498457	0.0711613038956	-6.5272744683E-6	0.827268381378	-0.0452597870997	0.001617107925	1.00097178364	0.0473129337088	0.579518583566	72.329	55.665	85.062
9	0.697308672157	-0.741911796369	-0.164929771225	2.59400428769	0.750993077526	1.57524027977	0.0201143100668	0.0575228342492	0.120064560832	-0.0264505839642	-0.0140923883248	-0.305196871396	0.0653978065329	-0.236827085367	6.63653072401E-5	0.492443767723	-0.209671381942	0.0166650783895	0.737615647368	0.0100965094742	0.525979716042	70.188	65.516	61.471
10	3.19968533446	0.895489593249	0.77094849888	0.733956051634	-0.557328580124	1.64857289536	0.410735570594	-0.0924505678871	0.31856926967	0.362137503847	-0.478418501438	0.329254124506	0.12794047745	-0.204110764302	-1.68454139818E-5	0.689666032276	-0.0242712093051	0.0179409925104	0.747660621684	-0.0491284073615	0.555658896836	49.867	63.458	60.274
11	1.34759590391	0.890503365188	-1.80559346002	1.42825326003	-0.754474338615	3.72965966947	0.375577111968	-0.678285760375	-0.501182780693	0.154461322868	-0.379052694467	-0.253719957289	1.00826150784	0.994570620835	-0.257949299859	0.784161011846	0.00601445045491	0.0423855434724	0.0675504679399	-0.0145826373965	0.676316866453	64.26	46.256	56.113
12	2.40077440491	-1.36509679402	0.757382968968	2.21821112691	-0.511621169601	3.30465086256	-0.272986146776	-0.637047531757	-0.177278048416	0.258302628038	0.456331821336	0.118532894574	-0.225653633513	-1.06858058695	0.231403949134	0.673495625554	-0.191004872705	-0.00415679872525	0.238155867232	0.108258510249	0.579871878037	40.924	52.296	51.308
13	4.13085042008	-0.00937192906415	0.887933247927	0.271756321594	0.386226824028	3.06692839369	-0.124212566814	-0.771572841384	0.299851171115	0.148365634949	0.083045734875	0.046857002648	-0.0328837975351	0.304841503206	-0.108099909059	0.334713765813	-0.277504570642	-0.0513447760036	-0.318659058981	-0.109405034021	0.586582551244	58.237	68.305	138.121
14	1.34088042866	0.649987242095	-1.42761778269	1.18652612755	-0.279287925357	1.70570562859	0.0697977182217	0.397406709134	0.131463672651	-0.443552172992	0.1847594406	-0.108017231071	-0.950104564072	-0.679223494595	0.0318695247467	0.88583057628	-0.161103534387	0.0662389186991	0.078070524559	0.00692059450879	0.612064566168	54.141	82.504	136.899
15	2.33703946984	0.217520506707	-0.0123161852768	1.5191492332	0.556739873713	2.43091687595	-0.109186064981	-0.401479129535	-0.274723624851	0.145216731521	0.188409154253	0.0390904267053	0.327758405911	0.0623179383863	-1.83649793269E-5	0.52417619634	-0.0943504642434	-0.0217451311091	0.776704513895	0.00958248707777	0.537741788952	49.569	59.62	148.254
16	2.14857546882	0.0671242073774	-1.52148265628	2.8281892436	0.984527363349	3.11732183487	-0.183437326568	-0.382545565749	0.242819845625	-0.0100893317081	0.0365286356942	0.064442575053	-0.0910687526576	0.101751278587	-0.00013457623782	0.489236579129	-0.138701554796	-0.0220369584254	0.70411356795	-0.0118243044016	0.503673091234	50.976	67.341	156.386
17	1.9878728911	-0.696780178722	-1.74226756788	0.123174367039	0.621777281219	1.64457139108	-0.13794737343	-0.30008396276	-0.188922574463	0.0822534829067	0.144859000189	-0.0747760521851	0.0528666153347	1.02393012836	-0.000276204254734	0.572911820858	-0.0859091026905	0.0238104656696	0.812091790151	0.0492694537149	0.573520429069	67.259	59.33	141.448
18	4.00103344869	-1.83951755549	-0.241694478973	1.0792866961	-0.24125252384	2.88050234351	0.109260446535	-0.00852858011011	-0.0654877160041	-0.333099607974	-0.0173415106083	-0.0562881755756	-0.1528854441	0.0648912744926	-1.30815710681E-5	0.523853556626	-0.251856592707	-0.0162668874732	0.435101716279	0.0151789478509	0.495923285218	54.153	56.626	112.286
19	0.991777029874	0.0239791585727	0.489276283212	0.307484381406	-0.473410580486	0.993750977811	-0.0629832338104	0.272878309783	-0.0139603497396	-0.198191166956	-0.167853706178	-0.145508442971	0.0390184407427	-0.406080060266	-0.000322623006	0.676510631803	-0.0861920245936	0.0530278407272	0.812348591432	-0.00207193044514	0.558132028293	43.465	61.008	97.307
20	1.64215088377	0.516979701011	-0.0854363803275	1.11231832632	-0.199395122088	0.905421517736	-0.158447680907	0.279879569025	-0.223692864494	-0.732361606142	0.056302082604	0.00865976887282	0.569557368837	-0.492700810723	-0.000112583777415	0.886602989691	-0.218548844498	-0.0484365244247	1.12821257217	-0.0206280655546	0.635072310077	35.663	55.292	76.071
21	2.26606478441	-0.129458117503	0.770777645435	2.57538451823	-1.1997680181	2.06139881573	0.0575144371641	0.493370609758	0.113114637825	-0.0163831528801	-0.0697917634905	0.274092243214	-0.246203103322	-0.349341224604	6.73858797822E-5	0.625609472394	-0.11453967109	0.0278699251406	0.886443561463	-0.0454673644182	0.529112760374	37.314	65.267	99.64
22	1.78899156186	-0.93185497044	0.860543454347	0.791806756563	-0.872724614208	1.959747895	-0.131566948444	0.10504151565	0.00867058152179	-0.0612007541264	0.191330135114	0.0100177623822	-0.0053904939751	0.263763663442	-9.12904882902	0.612424610612	-0.177335799337	-0.0240530659865	0.7058670799	-0.0424383156839	0.526194875331	57.669	63.489	100.763
23	2.34498201425	-0.930253376337	0.917041578077	1.16939787899	0.384865403754	0.895163317871	0.299387449106	0.492680283754	-0.517114718008	0.00167310870339	-0.0508850120081	0.21132223058	0.49520738687	-0.522065989185	-0.000657862166428	0.793404938935	-0.280476869042	0.0993005511672	0.86944148055	-0.0421316273244	0.711135161651	43.551	46.198	104.889
24	2.63600182567	0.202959614513	-0.873911713237	1.4907013221	-1.75250134197	2.21760196791	-0.0942707025716	0.105524030487	-0.37038077643	-0.307233490738	-0.0813094267741	-0.0563804629926	0.506143606955	0.557799703447	-5.15809859953E-5	0.64588932784	-0.0978172707178	0.0406987020482	0.911248042909	-0.109725265041	0.538606683903	66.854	52.435	109.846

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 9:58 )	A	9 - 58
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 59:108 )	A	59 - 108
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 109:158 )	A	109 - 158
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 159:208 )	A	159 - 208
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 209:258 )	A	209 - 258
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 259:308 )	A	259 - 308
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 309:358 )	A	309 - 358
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 359:408 )	A	359 - 408
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 409:458 )	A	409 - 458
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 459:508 )	A	459 - 508
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 509:558 )	A	509 - 558
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 559:597 )	A	559 - 597
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 9:58 )	B	9 - 58
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 59:108 )	B	59 - 108
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 109:158 )	B	109 - 158
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 159:208 )	B	159 - 208
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 209:258 )	B	209 - 258
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 259:308 )	B	259 - 308
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 309:358 )	B	309 - 358
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 359:408 )	B	359 - 408
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 409:458 )	B	409 - 458
22	X-RAY DIFFRACTION	22	( CHAIN B AND RESID 459:508 )	B	459 - 508
23	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 509:558 )	B	509 - 558
24	X-RAY DIFFRACTION	24	( CHAIN B AND RESID 559:597 )	B	559 - 597

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