PDB-8bz5: Crystal structure of the L. monocytogenes RmlT in complex with HEPES

ID or keywords:

Entry

Database: PDB / ID: 8bz5

Title

Crystal structure of the L. monocytogenes RmlT in complex with HEPES

Components

Glycosyltransferase

Keywords

TRANSFERASE / Glycosyltransferase

Function / homology

Function and homology information

Transferases; Glycosyltransferases / hexosyltransferase activity / biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Cereija, T.B. / Morais-Cabral, J.H.

Funding support

Portugal, 1items

Citation

Journal: Nat Commun / Year: 2025
Title: Molecular properties of the RmlT wall teichoic acid rhamnosyltransferase that modulates virulence in Listeria monocytogenes.
Authors: Monteiro, R. / Cereija, T.B. / Pombinho, R. / Voskuilen, T. / Codee, J.D.C. / Sousa, S. / Morais-Cabral, J.H. / Cabanes, D.

History

Deposition	Dec 14, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details 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 / _pdbx_entry_details.has_protein_modification
Revision 1.2	Feb 5, 2025	Group: Refinement description / Category: pdbx_initial_refinement_model Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bz5.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8bz5.ent.gz	823.8 KB	Display	PDB format
PDBx/mmJSON format	8bz5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bz5_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	8bz5_full_validation.pdf.gz	3.9 MB	Display
Data in XML	8bz5_validation.xml.gz	87.5 KB	Display
Data in CIF	8bz5_validation.cif.gz	118.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bz/8bz5 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/8bz5	HTTPS FTP

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Related structure data

Related structure data	8bz4SC 8bz6C 8bz7C 8bz8C 9gzjC 9gzkC S: Starting model for refinement 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	#254 - Feb 2021 Cellulose Synthase similarity (3) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Glycosyltransferase

B: Glycosyltransferase

C: Glycosyltransferase

D: Glycosyltransferase

hetero molecules

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

1

D: Glycosyltransferase

hetero molecules

A: Glycosyltransferase

hetero molecules

defined by author
Evidence: gel filtration
145 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glycosyltransferase

hetero molecules

B: Glycosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.081, 178.367, 92.154
Angle α, β, γ (deg.)	90.000, 93.515, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Glycosyltransferase Mass: 71637.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: APD94_03445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A401AAP7
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.36 Å³/Da / Density % sol: 47.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES-NaOH pH 7.5 20% (w/v) PEG 8,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980112 Å / Relative weight: 1
Reflection	Resolution: 2.3→48.12 Å / Num. obs: 116033 / % possible obs: 99.2 % / Redundancy: 7 % / B_iso Wilson estimate: 49.58 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.046 / R_rim(I) all: 0.121 / R_sym value: 0.112 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 7.2 % / R_merge(I) obs: 1.295 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5688 / CC_1/2: 0.596 / R_pim(I) all: 0.519 / R_rim(I) all: 1.396 / R_sym value: 1.295 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8BZ4

8bz4

Resolution: 2.3→48.12 Å / SU ML: 0.3148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2202	5697	4.91 %
R_work	0.193	110277	-
obs	0.1944	115974	99.11 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→48.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19534	0	270	502	20306

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0038	20235
X-RAY DIFFRACTION	f_angle_d	0.5859	27322
X-RAY DIFFRACTION	f_chiral_restr	0.6981	2940
X-RAY DIFFRACTION	f_plane_restr	0.004	3470
X-RAY DIFFRACTION	f_dihedral_angle_d	22.4891	7703

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	0.3038	199	0.2909	3628	X-RAY DIFFRACTION	98.97
2.33-2.35	0.3211	223	0.2912	3645	X-RAY DIFFRACTION	97.87
2.35-2.38	0.3398	204	0.2836	3610	X-RAY DIFFRACTION	99.66
2.38-2.41	0.3019	190	0.282	3655	X-RAY DIFFRACTION	97.71
2.41-2.44	0.3238	198	0.2802	3677	X-RAY DIFFRACTION	99.61
2.44-2.48	0.3356	181	0.2791	3613	X-RAY DIFFRACTION	98.34
2.48-2.51	0.3268	176	0.2786	3647	X-RAY DIFFRACTION	98.94
2.51-2.55	0.307	186	0.2687	3739	X-RAY DIFFRACTION	99.12
2.55-2.59	0.2905	171	0.2556	3617	X-RAY DIFFRACTION	98.65
2.59-2.63	0.2954	193	0.255	3713	X-RAY DIFFRACTION	99.34
2.63-2.68	0.293	181	0.262	3607	X-RAY DIFFRACTION	98.7
2.68-2.73	0.3011	191	0.2631	3702	X-RAY DIFFRACTION	98.96
2.73-2.78	0.3043	184	0.2674	3657	X-RAY DIFFRACTION	99.25
2.78-2.84	0.3266	181	0.2924	3680	X-RAY DIFFRACTION	98.57
2.84-2.9	0.3318	186	0.2806	3667	X-RAY DIFFRACTION	99.84
2.9-2.97	0.2583	170	0.2442	3693	X-RAY DIFFRACTION	98.85
2.97-3.04	0.2685	186	0.2313	3699	X-RAY DIFFRACTION	99.11
3.04-3.12	0.2408	207	0.215	3659	X-RAY DIFFRACTION	99.74
3.12-3.21	0.2332	200	0.2057	3645	X-RAY DIFFRACTION	99.15
3.21-3.32	0.2483	186	0.2066	3687	X-RAY DIFFRACTION	99.26
3.32-3.44	0.2201	178	0.2104	3719	X-RAY DIFFRACTION	99.36
3.44-3.57	0.2079	213	0.1816	3676	X-RAY DIFFRACTION	99.44
3.57-3.74	0.1899	186	0.1766	3705	X-RAY DIFFRACTION	99.44
3.74-3.93	0.2172	172	0.162	3691	X-RAY DIFFRACTION	99.59
3.93-4.18	0.1909	191	0.1628	3715	X-RAY DIFFRACTION	99.57
4.18-4.5	0.1795	182	0.1467	3679	X-RAY DIFFRACTION	99.54
4.5-4.95	0.1568	214	0.1378	3693	X-RAY DIFFRACTION	99.47
4.95-5.67	0.1745	188	0.1519	3714	X-RAY DIFFRACTION	99.69
5.67-7.14	0.2145	182	0.1759	3723	X-RAY DIFFRACTION	99.06
7.14-48.12	0.156	198	0.1474	3722	X-RAY DIFFRACTION	98.67

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	4.72427655878	-0.0640244625548	0.821624819008	2.01180142017	0.809259118976	6.19291152646	-0.0443763654108	-0.140121699285	0.316557703659	-0.0253181675661	0.111248929885	-0.4508715706	-0.385839239041	0.746528128204	-0.0467162641247	0.432388135163	0.0374233714113	0.0709220525391	0.385297852381	0.0242381156418	0.402815450786	-3.67205186812	-32.5530515428	-14.9805937911
2	1.17423469509	-0.528167169408	-0.33430399539	2.03864283569	-0.742279925512	3.45104328058	-0.0756446442363	0.124613028193	-0.03031351265	-0.241318150582	-0.0458751757916	-0.216976861245	0.326947565626	0.165641587953	0.146901919908	0.329956388245	0.0102308921389	0.0357488983055	0.341239164007	0.0184228037222	0.395844138591	-11.7591242254	-33.2677448667	-31.1878055513
3	1.13334784674	-0.25928529336	-0.663331272316	0.991161082691	0.0784182879315	1.53154530747	-0.0273685124568	0.112215879242	-0.0496223819031	-0.157050876824	-0.0159010702909	0.171201227079	0.118643949992	-0.106318029897	0.0346116221056	0.286758652428	-0.00168035494262	-0.0128862700469	0.29991520145	0.00183295422335	0.365882720348	-32.7434001086	-22.3943597866	-33.8090597733
4	3.51602755606	1.27893172484	0.478216499618	6.73277367416	3.42402953961	7.89498592379	-0.140087781985	-0.792656763319	0.235096913396	0.591834304126	0.106999121022	-0.0844477149513	-0.172664741096	0.0884880673183	0.0791277459114	0.557400218302	0.159995388915	0.076742061519	0.649356481339	0.00111535458231	0.466599219133	-40.7329606883	-14.1480206629	11.8675881889
5	2.92467085342	0.836527611905	-0.62249452992	2.62678741816	-0.197531937349	1.75237446403	-0.0638532307306	-0.0396264676212	-0.262086260655	0.0123224181426	0.0268540985125	0.0967052376315	0.328136597456	-0.0611192893293	0.0494610773699	0.400098647813	0.0316700480626	-0.0211856758505	0.337589596012	0.0135670755225	0.290864230984	-10.0495051121	-32.1623404487	15.4901718914
6	0.701191710484	0.51588685487	1.31380779829	2.17223775144	0.388614347417	3.36501235953	0.0369796353227	-0.227454658084	-0.191401900059	0.263688409018	0.129363540803	-0.118352331786	0.269825136034	0.101148632686	-0.165792332396	0.273538847545	0.0547831872787	0.0228268355575	0.448742454228	0.0684856867743	0.375418486817	3.15376189253	-28.1864234715	27.4971943379
7	1.11772723461	-0.124849607176	0.588871076791	1.39337273763	-0.640255541418	2.46560986084	-0.130132343956	-0.107833045291	0.0420752455575	0.140127391006	0.0865312693359	-0.156685294362	-0.196811645247	0.210008618466	0.0511923709733	0.299234233012	0.0404849356861	0.00733346828279	0.315896766377	0.0015928864431	0.381322223268	6.93205122774	-2.9199787612	19.8431867014
8	6.4285087418	-2.04484492396	3.08692668487	3.23620419482	-0.937493802551	5.38667996692	-0.105435794527	0.770860208606	0.312430030043	-0.410794474203	-0.0283105664715	0.63174712287	-0.378704602015	-0.45600939624	0.102199684398	0.557094162113	-0.0474369471858	-0.165655350568	0.554965234647	0.128209275011	0.565210462896	-20.5964973921	2.02953739422	-16.8982923404
9	3.96881701152	0.436650448026	-0.135000670077	3.09244669642	0.672809372336	3.546290762	-0.0372695237876	0.284267768459	0.164370028471	-0.291660611035	0.256257826353	-0.579053196208	-0.0061804257996	0.872851489009	-0.219569521957	0.427640776056	-0.0102912932574	0.0952095146956	0.566084902908	-0.0676351967824	0.538254051684	30.9270367892	-50.3392020505	-30.833375695
10	2.86048309657	1.25996599488	0.842620722259	2.07694301741	-0.489705363283	4.25510403755	0.326433930535	-0.369755617064	-0.118273083899	0.280486593154	-0.175304442345	-0.50124679582	0.0267203490352	0.530033857749	-0.0941157036394	0.372342351801	-0.0194845157225	0.0082107956832	0.50665846084	-0.0611129308059	0.632059872257	27.1610424351	-50.3633878835	-15.4247118895
11	1.15005583953	0.133294285278	-0.0317842091628	1.10997208089	0.113187650162	1.58430627561	0.137244675387	-0.0712864881218	0.0737742057604	0.286019390277	-0.0470200725015	0.041448338264	-0.0838576481774	0.0318682155833	-0.0675378053328	0.413125222554	-0.0376055551799	0.0408965315193	0.265207427768	-0.0214208197547	0.368637157827	4.86257175411	-63.2770065482	-13.8449531861
12	1.60649573802	-0.3991450491	-0.479806436344	2.13874311066	0.887860204996	2.84943055196	0.0837840465502	0.529014611428	-0.209688217534	-0.317945188039	-0.145577343183	-0.0549828392392	0.182116927448	-0.403444447879	0.0099137171008	0.551557218992	0.0411599212461	-0.0382307501113	0.864497586667	-0.150853784148	0.49289930189	0.876130476279	-76.6251905807	-58.9602247689
13	5.07871875365	-2.42063694395	0.723200451644	2.83451781677	-2.15485759878	6.34126423125	-0.188376397811	0.391303807888	0.121103270016	-0.305245824952	-0.0518259220872	0.759821677347	-0.375804058228	-0.999482056092	0.2629997949	0.689625157436	0.0465714290259	-0.0790116783016	0.513946480915	-0.0815728431814	0.788458955517	-48.7123604141	-47.4663453494	21.6114063117
14	3.22794298095	1.48464819233	-1.99881978572	5.22786453856	0.0652109525707	3.17367628724	0.0726028199146	0.14575069183	0.295758315691	-0.282994944418	0.0564971071996	-0.0248474293015	-0.504097570148	-0.041265479329	-0.132745940755	0.411170496396	0.00640162819232	-0.0393811110179	0.345289494829	0.00728701018534	0.376309707413	-32.4879803784	-59.4826591411	23.6388412953
15	0.582666633049	-0.114125802213	-1.3251136153	1.32761526013	0.422155880701	3.52166362696	-0.0936267495961	0.114984140165	0.184877487392	-0.306215105723	0.0749175558805	-0.0871843486169	-0.297389582254	-0.0040837014356	-0.0850368491052	0.556193381926	-0.0495348527779	-0.00938251686916	0.419485271059	-0.00841483036984	0.485871073994	-30.2799549995	-68.2321274439	9.58735310949
16	1.08563702795	0.154323346741	-0.878763184347	0.546964710682	-0.151497679928	1.42947978736	-0.0897980578881	-0.0316755302453	-0.0260787386868	-0.00752380261137	0.0515608289124	-0.0677229072914	-0.000477222308968	0.0368987847444	0.0697713586287	0.327346313466	-0.0140374113925	-0.0267182556067	0.339916533708	-0.024512877276	0.421473028603	-40.2360523041	-85.1757649202	35.0264848447

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 16 through 141 )	A	A	16 - 141	1 - 126
2	2	chain 'A' and (resid 142 through 255 )	A	A	142 - 255	127 - 235
3	3	chain 'A' and (resid 256 through 523 )	A	A	256 - 523	236 - 503
4	4	chain 'A' and (resid 524 through 623 )	A	A	524 - 623	504 - 603
5	5	chain 'B' and (resid 17 through 162 )	B	B	17 - 162	1 - 146
6	6	chain 'B' and (resid 163 through 273 )	B	B	163 - 273	147 - 250
7	7	chain 'B' and (resid 274 through 523 )	B	B	274 - 523	251 - 500
8	8	chain 'B' and (resid 524 through 623 )	B	B	524 - 623	501 - 600
9	9	chain 'C' and (resid 16 through 162 )	C	C	16 - 162	1 - 147
10	10	chain 'C' and (resid 163 through 255 )	C	C	163 - 255	148 - 240
11	11	chain 'C' and (resid 256 through 523 )	C	C	256 - 523	241 - 508
12	12	chain 'C' and (resid 524 through 623 )	C	C	524 - 623	509 - 608
13	13	chain 'D' and (resid 17 through 108 )	D	D	17 - 108	1 - 89
14	14	chain 'D' and (resid 109 through 219 )	D	D	109 - 219	90 - 200
15	15	chain 'D' and (resid 220 through 273 )	D	D	220 - 273	201 - 248
16	16	chain 'D' and (resid 274 through 623 )	D	D	274 - 623	249 - 598

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-Structure viewers

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

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-Experimental details

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-Data collection

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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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

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi