PDB-6yuv: Capsule O-acetyltransferase of Neisseria meningitidis serogroup A

ID or keywords:

Entry

Database: PDB / ID: 6yuv

Title

Capsule O-acetyltransferase of Neisseria meningitidis serogroup A

Components

SacC

Keywords

TRANSFERASE / O-acetyltransferase / a/b hydrolase fold / serine transferase / catalytic triad

Function / homology

Uncharacterised protein family (UPF0227) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / TRIETHYLENE GLYCOL / SacC

Function and homology information

Biological species

Neisseria meningitidis serogroup A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Cramer, J.T. / Fiebig, T. / Fedorov, R. / Muehlenhoff, M.

Funding support

Germany, 2items

Citation

Journal: Nat Commun / Year: 2020
Title: Structural and mechanistic basis of capsule O-acetylation in Neisseria meningitidis serogroup A.
Authors: Fiebig, T. / Cramer, J.T. / Bethe, A. / Baruch, P. / Curth, U. / Fuhring, J.I. / Buettner, F.F.R. / Vogel, U. / Schubert, M. / Fedorov, R. / Muhlenhoff, M.

History

Deposition	Apr 27, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2020	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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 24, 2024	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	6yuv.cif.gz	255.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6yuv.ent.gz	172.8 KB	Display	PDB format
PDBx/mmJSON format	6yuv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6yuv_validation.pdf.gz	1019.7 KB	Display	wwPDB validaton report
Full document	6yuv_full_validation.pdf.gz	1020.4 KB	Display
Data in XML	6yuv_validation.xml.gz	19.9 KB	Display
Data in CIF	6yuv_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yu/6yuv ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yuv	HTTPS FTP

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Related structure data

Related structure data	6yuoSC 6yuqC 6yusC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6yuo-1 6yus-1 6yuq-1 21440 2aeg-d 5xmb-d 3oml-1 6a97-d 1hyn-d 5kx6-d 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: SacC

B: SacC

hetero molecules

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

1

A: SacC

B: SacC

hetero molecules

A: SacC

B: SacC

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation
118 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.320, 138.320, 70.560
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
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	SacC Mass: 29374.439 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup A (bacteria) Gene: sacC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O68216
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.87 Å³/Da / Density % sol: 57.18 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor ...Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor contained 50 mM HEPES pH 7.0, 100 mM HEPES pH 7.6, 100 mM NaCl, 5 mM MgCl2, 1 mM EDTA, and 31-42% PEG200.

Crystal

Density Matthews: 2.87 Å³/Da / Density % sol: 57.18 %

Crystal grow

Temperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Native wild type CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID30B / Wavelength: 0.999996 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.999996 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 46740 / % possible obs: 100 % / Redundancy: 22.8 % / B_iso Wilson estimate: 50.533 Å² / CC_1/2: 1 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.01 / R_rim(I) all: 0.049 / Net I/σ(I): 36.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2-2.07	22.9	0.694	5	4601	0.977	0.148	0.71	99.9
2.07-2.15	22.1	0.5	7.1	4582	0.983	0.108	0.512	99.9
2.15-2.25	24	0.325	11.1	4615	0.993	0.068	0.332	100
2.25-2.37	23.6	0.221	15.8	4596	0.997	0.046	0.226	100
2.37-2.52	23.2	0.147	22.6	4650	0.998	0.031	0.15	100
2.52-2.71	23.4	0.105	31	4653	0.999	0.022	0.107	100
2.71-2.99	24.3	0.07	45.7	4646	0.999	0.014	0.071	100
2.99-3.42	22.1	0.05	60.6	4679	1	0.011	0.052	100
3.42-4.31	22.3	0.038	77.2	4760	1	0.008	0.039	100
4.31-57.25	20.5	0.032	80.5	4958	1	0.007	0.033	100

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.18	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YUO

6yuo

Resolution: 2→49.4 Å / SU ML: 0.2127 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2813

	R_factor	Num. reflection	% reflection
R_free	0.2072	2334	5 %
R_work	0.1792	-	-
obs	0.1806	46709	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 55.41 Å²

Refinement step

Cycle: LAST / Resolution: 2→49.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3915	0	12	165	4092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0079	4006
X-RAY DIFFRACTION	f_angle_d	0.8053	5425
X-RAY DIFFRACTION	f_chiral_restr	0.0548	615
X-RAY DIFFRACTION	f_plane_restr	0.0043	683
X-RAY DIFFRACTION	f_dihedral_angle_d	15.6276	1452

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 (%)
2-2.04	0.2922	136	0.2525	2569	X-RAY DIFFRACTION	99.63
2.04-2.09	0.2995	134	0.2295	2555	X-RAY DIFFRACTION	99.78
2.09-2.13	0.289	134	0.2262	2569	X-RAY DIFFRACTION	99.82
2.13-2.19	0.2586	136	0.2198	2568	X-RAY DIFFRACTION	99.85
2.19-2.25	0.2286	135	0.2131	2572	X-RAY DIFFRACTION	99.85
2.25-2.31	0.2754	136	0.203	2575	X-RAY DIFFRACTION	99.93
2.31-2.39	0.26	137	0.2013	2594	X-RAY DIFFRACTION	99.93
2.39-2.47	0.2636	135	0.1991	2564	X-RAY DIFFRACTION	99.96
2.47-2.57	0.211	136	0.1992	2586	X-RAY DIFFRACTION	100
2.57-2.69	0.2436	136	0.204	2595	X-RAY DIFFRACTION	99.93
2.69-2.83	0.2254	138	0.1944	2617	X-RAY DIFFRACTION	100
2.83-3.01	0.236	137	0.2032	2601	X-RAY DIFFRACTION	99.93
3.01-3.24	0.2602	137	0.2068	2629	X-RAY DIFFRACTION	99.96
3.24-3.57	0.2381	138	0.1944	2618	X-RAY DIFFRACTION	100
3.57-4.08	0.1494	141	0.1631	2660	X-RAY DIFFRACTION	100
4.08-5.14	0.1528	140	0.141	2672	X-RAY DIFFRACTION	100
5.14-49.4	0.1997	148	0.1617	2831	X-RAY DIFFRACTION	99.9

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	4.09446748508	0.766036134551	-4.62641901117	5.68647127596	-0.786464904486	8.3999550796	-0.319025556374	0.540073984243	-1.07440015549	-0.367683928635	0.193853124442	-1.00798611781	0.970021504197	2.14196447317	0.000539202347423	0.450974434753	0.115601579417	0.0186981219418	0.98963141932	-0.293274984914	0.749887234585	11.0768414422	29.6347318195	-24.6152798974
2	3.15552816173	-0.546044782996	0.471783937367	2.49999317771	0.297145925394	3.06249799722	-0.0393312609613	0.636258691654	-0.366501610214	-0.37177436932	0.260385345134	-0.26024774648	0.119853940269	0.616227067702	-0.262505280729	0.371647839117	-0.000393486490891	0.0430446574476	0.638707323769	-0.197262253737	0.421950788503	2.12678803257	35.2279590471	-29.3076779385
3	6.80497325092	0.381062643036	-0.237251842734	4.91307910829	1.04704583068	5.07132762387	-0.0497641244505	0.606389153627	-0.675968029382	-0.159215734241	0.27696297216	-0.502183634794	0.154710057815	0.927859433414	-0.183891451268	0.381192495399	0.0343833464116	0.00281213873547	0.547124668407	-0.147122699742	0.31111400782	-3.08976751333	34.1080329402	-28.2500251217
4	3.81067395857	0.226143869248	1.11638499555	2.15945428307	-0.283818633008	4.51866470022	-0.220165157357	0.391482735862	-0.00333480766664	-0.194277635116	0.310050983806	-0.128362292317	-0.297814568521	0.570137502063	-0.0752898489606	0.378624621526	-0.0496402612295	0.0259682104395	0.383737696447	-0.0402922561959	0.292964034376	-6.36882092385	42.6293142292	-26.4320751827
5	8.58234021808	0.301074134074	-1.91483474082	4.27312606634	-0.16652419197	5.18888273858	-0.0756845643206	0.110044204785	-1.16075476692	0.132644089368	0.0707730805865	0.164098893288	0.562091496964	-0.511166889516	0.00996823084241	0.471160607223	-0.0888226676539	-0.0469924038911	0.372429339736	0.013356880607	0.441544805879	-23.3849056516	28.0444850752	-26.2208001006
6	3.10926579263	-0.745571218196	0.234534275196	3.21738687237	0.845862635159	3.1806428908	-0.264007011343	0.546518840417	0.17010600963	-0.491201764214	0.149132206133	0.245957939644	-0.460344653308	-0.00220939495739	0.103727397828	0.474213863379	-0.108981073058	-0.0859490349785	0.334414044641	0.072137509497	0.331624006959	-16.281181516	49.1608282382	-31.4665738568
7	2.84090232636	-0.514928211693	-2.06614071088	3.26518804689	0.813400124749	5.82248656187	0.10519690791	0.787887961381	0.16377770335	-0.989558488272	0.256865392945	-0.104637454618	-0.819942914704	0.204133180566	-0.310928290701	0.628164500247	-0.223970097294	-0.063532667987	0.765036961818	0.0869293981728	0.44098068166	-11.0895268673	50.5580073423	-40.0559060683
8	6.21043403623	-0.120567459373	0.447247095911	6.92591505292	0.420973821532	6.95945247046	-0.253657054697	0.795346551387	0.341717846322	-1.19717576507	0.54583749897	-0.66569121716	-0.461760023277	1.51702315217	-0.237736147595	0.62811040527	-0.225137890333	0.134038529559	0.926338484661	-0.000840087997203	0.396102412562	0.230010950045	48.5903561672	-40.6853054417
9	0.863175575313	1.53338378761	-1.70554086141	3.78013651051	-0.190071830898	9.40706437885	0.0772255850195	-0.0150145342106	0.0668085525545	0.0375434310359	0.048012221722	0.142520550893	-0.317615451501	-0.00485362496123	-0.0845587076003	0.246988480854	0.0905310116446	-0.0575471931324	0.376355665625	-0.0860849399927	0.408455693519	4.59540988195	46.8008197125	-4.35032711861
10	3.12809146942	2.02672199043	-2.38709578291	2.51467494437	-1.29543115201	5.25602838548	0.240738259744	-0.356424531396	-0.186292887792	0.0499256873845	-0.253433338022	-0.227230000287	-0.00790422277543	0.443433665362	-0.00830936976506	0.301921211139	0.0502066157596	-0.0903470274999	0.33306029259	-0.0825279328805	0.375365734033	3.58192647098	38.0858723125	4.40580376551
11	4.73882082824	0.470438336176	-3.80488190405	4.48941585758	0.836742934487	6.56468799079	0.146959793976	0.0730166498355	-0.0708776572853	0.130465070157	-0.112798986204	-0.0112132447183	0.0171139333753	0.105663038438	0.00767185360493	0.297463275948	0.0606082199392	-0.041013454945	0.263968654408	-0.0608907927017	0.345414588118	-0.706546575073	37.4611513544	-0.661107325826
12	2.53300274265	1.55927185353	0.342559840288	2.12673119985	-1.58964358549	2.71756970967	0.0122391432668	0.187758479604	-0.739978084034	-0.399577503577	-0.238665809172	-0.376786735954	0.724040049619	0.869767335786	0.207888852604	0.428480769116	0.182802169843	-0.0286122585075	0.581284901542	-0.0548217361353	0.667535365279	9.67661697852	28.8256425221	-1.9140755075
13	4.70492603369	1.3795708303	1.04869130018	2.50682096755	-1.28935492018	3.76416250806	0.0408966093413	-0.0940279447001	-0.164272427293	0.156362541771	-0.0745983791363	0.111128512305	0.34802716599	-0.131557042532	0.0481598203297	0.394261527164	-0.0024275578001	-0.00584598431965	0.336820605816	-0.0691479379526	0.379732719721	-8.09461481999	29.8482777039	4.59401289739
14	5.95879651859	-1.53616343674	1.77579265057	1.71395134504	-1.25314617043	3.0792121499	0.0859513521484	0.154131719558	-0.813154310755	0.00664837805737	-0.045266787676	0.216492900317	0.750654639604	-0.122629529196	-0.0367403730622	0.557321344154	-0.0505562229686	0.0146836101276	0.341322893093	-0.0775819222738	0.475029867937	-9.28824450621	22.7368399798	2.94733577881
15	4.65554782736	-0.280167312103	-0.906300163871	5.35912655116	0.562462942507	7.0628064403	0.0242703668447	-0.425933188019	-0.977477824664	0.360990239994	-0.0753310187278	0.116938188355	1.33723458075	0.0707572812554	0.0815599697859	0.567634192978	0.00399186165939	0.00993393098413	0.398975508938	0.0848865055662	0.531534082772	-2.27303084364	18.5948681875	11.7926476532
16	6.80546375244	1.52951305406	-6.92183173849	4.04180826486	-0.477972836459	2.0849361401	-0.162743593501	-1.02063972551	-0.25369534959	0.268425820588	0.018556789345	-0.63632483544	0.388547483412	1.91099162419	0.235313438027	0.558909030144	0.159734544985	-0.151791523382	0.726130773895	0.00805339223168	0.535807514932	10.4512845454	29.1958618891	13.711066845
17	2.00012775948	1.99966029791	1.9997866784	2.0000968912	0.800808922838	2.0000007351	2.22671414846	4.41347096004	2.9183295167	-3.2720227878	-2.63938885535	3.35518431473	-2.00677314929	-1.22917979384	0.415678996029	0.945276699356	0.591293274642	-0.131234269681	1.37060456335	-0.021612220894	1.55076801097	20.0103474478	23.1815787774	7.22825846241

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 1 through 15 )	A	A	1 - 15	1 - 15
2	2	chain 'A' and (resid 16 through 51 )	A	A	16 - 51	16 - 51
3	3	chain 'A' and (resid 52 through 87 )	A	A	52 - 87	52 - 87
4	4	chain 'A' and (resid 88 through 148 )	A	A	88 - 148	88 - 148
5	5	chain 'A' and (resid 149 through 172 )	A	A	149 - 172	149 - 172
6	6	chain 'A' and (resid 173 through 215 )	A	A	173 - 215	173 - 215
7	7	chain 'A' and (resid 216 through 229 )	A	A	216 - 229	216 - 229
8	8	chain 'A' and (resid 230 through 246 )	A	A	230 - 246	230 - 246
9	9	chain 'B' and (resid 1 through 27 )	B	B	1 - 27	1 - 27
10	10	chain 'B' and (resid 28 through 47 )	B	B	28 - 47	28 - 47
11	11	chain 'B' and (resid 48 through 100 )	B	B	48 - 100	48 - 100
12	12	chain 'B' and (resid 101 through 114 )	B	B	101 - 114	101 - 114
13	13	chain 'B' and (resid 115 through 160 )	B	B	115 - 160	115 - 160
14	14	chain 'B' and (resid 161 through 198 )	B	B	161 - 198	161 - 198
15	15	chain 'B' and (resid 199 through 229 )	B	B	199 - 229	199 - 229
16	16	chain 'B' and (resid 230 through 245 )	B	B	230 - 245	230 - 245
17	17	chain 'B' and (resid 246 through 246 )	B	B	246	246

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