PDB-7a5q: Crystal structure of VcSiaP bound to sialic acid

ID or keywords:

Entry

Database: PDB / ID: 7a5q

Title

Crystal structure of VcSiaP bound to sialic acid

Components

DctP family TRAP transporter solute-binding subunit

Keywords

TRANSPORT PROTEIN / TRAP transporter / substrate binding protein / transporter

Function / homology

Function and homology information

transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Schneberger, N. / Peter, M.F. / Hagelueken, G.

Funding support

Germany, 1items

Citation

Journal: J.Mol.Biol. / Year: 2020
Title: Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates.
Authors: Peter, M.F. / Gebhardt, C. / Glaenzer, J. / Schneberger, N. / de Boer, M. / Thomas, G.H. / Cordes, T. / Hagelueken, G.

History

Deposition	Aug 21, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 13, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2	Jan 31, 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	7a5q.cif.gz	315.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7a5q.ent.gz	213.9 KB	Display	PDB format
PDBx/mmJSON format	7a5q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7a5q_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	7a5q_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7a5q_validation.xml.gz	31.5 KB	Display
Data in CIF	7a5q_validation.cif.gz	43.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a5/7a5q ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a5q	HTTPS FTP

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Related structure data

Related structure data	7a5cC 3b50S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4mnp-d 6md2-1 3bc5-d 6mcz-1 3kdu-2 6l36-1 3kdt-2 6kyp-2 4p56-3 4p1l-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	#198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: DctP family TRAP transporter solute-binding subunit

B: DctP family TRAP transporter solute-binding subunit

hetero molecules

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

1

A: DctP family TRAP transporter solute-binding subunit

hetero molecules

defined by author
Evidence: gel filtration
35 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DctP family TRAP transporter solute-binding subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.354, 106.738, 134.506
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 2 molecules AB

#1: Protein	DctP family TRAP transporter solute-binding subunit / Sialic acid-binding protein Mass: 33790.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: C9J66_17385, GQX72_05445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H5WZA5, UniProt: Q9KR64*PLUS

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Sugars , 2 types, 3 molecules

#2: Sugar

ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID

Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DNeup5Acb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-neuraminic acid	COMMON NAME	GMML 1.0
b-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₆H₁₂O₆

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Non-polymers , 3 types, 329 molecules

#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.57 Å³/Da / Density % sol: 52.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus Screen (Molecular Dimensions) condition F4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000009 Å / Relative weight: 1
Reflection	Resolution: 1.68→45.5 Å / Num. obs: 152174 / % possible obs: 99.6 % / Redundancy: 7.2 % / B_iso Wilson estimate: 23.73 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 7.1
Reflection shell	Resolution: 1.68→1.74 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.92 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7732 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHASER		phasing
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3B50

3b50

Resolution: 1.68→45.5 Å / SU ML: 0.2309 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 30.2903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2469	7587	5 %
R_work	0.2127	144228	-
obs	0.2144	151815	99.13 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.92 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→45.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4738	0	212	304	5254

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0185	5121
X-RAY DIFFRACTION	f_angle_d	1.8086	6907
X-RAY DIFFRACTION	f_chiral_restr	0.23	760
X-RAY DIFFRACTION	f_plane_restr	0.0118	881
X-RAY DIFFRACTION	f_dihedral_angle_d	21.3003	1937

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 (%)
1.68-1.7	0.3706	232	0.3862	4410	X-RAY DIFFRACTION	90
1.7-1.72	0.4172	251	0.368	4655	X-RAY DIFFRACTION	96.73
1.72-1.74	0.3883	249	0.348	4779	X-RAY DIFFRACTION	98.94
1.74-1.76	0.3259	257	0.3177	4803	X-RAY DIFFRACTION	99.65
1.76-1.79	0.3248	263	0.3019	4889	X-RAY DIFFRACTION	99.73
1.79-1.81	0.3316	249	0.2767	4845	X-RAY DIFFRACTION	99.8
1.81-1.84	0.2677	254	0.2568	4802	X-RAY DIFFRACTION	99.84
1.84-1.86	0.256	260	0.2418	4895	X-RAY DIFFRACTION	99.85
1.86-1.89	0.2586	252	0.2311	4775	X-RAY DIFFRACTION	99.82
1.89-1.92	0.229	257	0.2239	4849	X-RAY DIFFRACTION	99.71
1.92-1.96	0.2263	249	0.2132	4864	X-RAY DIFFRACTION	99.77
1.96-1.99	0.2442	259	0.2062	4795	X-RAY DIFFRACTION	99.65
1.99-2.03	0.2229	250	0.2081	4852	X-RAY DIFFRACTION	99.73
2.03-2.07	0.2191	257	0.2052	4834	X-RAY DIFFRACTION	99.69
2.07-2.12	0.2183	256	0.2075	4853	X-RAY DIFFRACTION	99.34
2.12-2.17	0.2133	256	0.1955	4781	X-RAY DIFFRACTION	99.55
2.17-2.22	0.251	251	0.1946	4801	X-RAY DIFFRACTION	98.86
2.22-2.28	0.2376	257	0.1894	4839	X-RAY DIFFRACTION	99.88
2.28-2.35	0.2559	256	0.1867	4837	X-RAY DIFFRACTION	99.73
2.35-2.42	0.242	259	0.1876	4866	X-RAY DIFFRACTION	99.81
2.42-2.51	0.2458	247	0.1918	4808	X-RAY DIFFRACTION	99.78
2.51-2.61	0.2355	251	0.1887	4841	X-RAY DIFFRACTION	99.76
2.61-2.73	0.2401	249	0.1959	4871	X-RAY DIFFRACTION	99.69
2.73-2.87	0.2656	249	0.1905	4812	X-RAY DIFFRACTION	99.61
2.87-3.05	0.2277	251	0.1919	4828	X-RAY DIFFRACTION	99.34
3.05-3.29	0.2117	250	0.1953	4751	X-RAY DIFFRACTION	98.43
3.29-3.62	0.1995	256	0.1899	4859	X-RAY DIFFRACTION	99.9
3.62-4.14	0.2249	255	0.188	4839	X-RAY DIFFRACTION	99.82
4.14-5.22	0.2569	250	0.2112	4825	X-RAY DIFFRACTION	99.45
5.22-45.5	0.2885	255	0.2631	4770	X-RAY DIFFRACTION	98.26

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	2.71735731342	-0.378624210329	0.998489174389	6.30754465938	0.197509430456	1.57262100655	0.0486101976422	0.150691439678	0.601475368041	0.0410525106894	0.0444310323282	-0.166120624457	-0.717685582574	0.0888799753495	-0.0482082885507	0.415314581134	-0.0203786204856	0.075400733907	0.176917739819	0.0167351504876	0.372520862543	18.123180684	19.0657278023	19.5172811275
2	1.46999032371	0.523606857726	-0.521232261191	1.17669996831	0.0526828411734	1.4491760556	0.112002711388	0.092554460214	0.084015179935	0.0694609104108	-0.040862767794	0.0757544339859	-0.223687273869	-0.141219640496	-0.0354801200521	0.204540832306	0.0602627825772	0.00839239968364	0.197744926141	-0.00453517821434	0.21795243047	8.21200076689	2.97283064425	22.7717754524
3	4.11155444306	-1.52563170914	-0.98456332381	4.66378311891	4.60424682632	8.57122162768	0.254412231164	0.568769469106	0.396487387327	-0.252115834061	-0.223476397996	0.292997477656	-0.507142260235	-0.641414393271	-0.0560244719188	0.212782675979	0.0844776767548	0.03149679512	0.327157535665	0.0710683203359	0.31285473244	-1.58714206509	5.84553573845	15.2074546644
4	0.878924571273	-0.63647041516	-0.362369247481	2.20785268745	0.684452425729	1.31261285849	0.00776641117768	-0.0381161588932	-0.00548722472849	0.135705868533	0.0365006834075	-0.0550396020572	-0.0110810424798	0.0804690133896	-0.0310448859726	0.122572812848	0.0117003986121	-0.0101254785575	0.148247534939	-0.00563153506773	0.162072018222	19.1151363013	-7.81606524913	16.3809308519
5	2.40156558541	-3.36360677094	-1.46370837615	6.15109243713	2.35214340279	2.13335344899	0.185309947692	0.127300989538	0.248595565128	-0.326129831013	-0.0874799192367	0.00413940080258	-0.540576286054	-0.20744175503	-0.11927845269	0.305470639223	0.0314411564625	0.00514981452438	0.157259441303	0.0246567174766	0.251994078138	12.398177852	13.0635452463	12.9931433167
6	7.31285413502	-1.77782857427	-3.23648058612	1.84509286575	0.228795754811	2.76461305103	-0.0950232147236	0.32151195255	-0.0993804831119	-0.0748948932578	0.0316120472176	0.432885374027	0.0447839875113	-0.477260504363	0.0644318949406	0.152459552074	-0.0130072128155	-0.0498340208223	0.228519029517	-0.0111624046986	0.255387484291	4.91784815802	-12.3668783734	10.2230068525
7	3.03380341299	0.319683020085	0.211281329721	5.08086231784	0.491549163902	2.1258860305	-0.0501701450745	0.0743411518283	0.606867441721	-0.201285712105	0.148941611566	0.336818807613	-0.779718083918	0.00798085305965	-0.0840150492583	0.397952125801	0.0282011136663	0.0369391191334	0.171586931318	0.0114666506224	0.3529038949	5.99917845428	11.9835340088	-19.7134432584
8	1.0912788504	-0.212644258217	-0.223278757556	1.63989065352	-0.428378932729	1.67385666887	0.0179446618325	0.0261307611005	0.0664261913105	-0.17817709425	-0.0338275987355	-0.0980436361063	-0.163659402204	0.104276943493	0.0144401852287	0.20347711844	-0.0285967797916	-0.00673936840241	0.182048960381	0.0100583502366	0.215493364427	15.8711178752	-3.8727837058	-23.1099714282
9	2.40642603593	0.473879469437	-1.05862926118	3.67274993479	-5.30078668427	9.15126998882	-0.108080993686	-0.0200571813885	0.280247777953	0.0560657433704	-0.103279855943	-0.241162392177	-0.415342234158	0.354360315955	0.167397536792	0.199032929636	-0.0881281830936	-0.00567902012148	0.219602889642	-0.0344165131378	0.225866716856	25.8419363546	-1.08749417333	-15.6147664381
10	0.98296477162	0.931665001603	-0.415929810952	2.44864739201	-0.811299651798	1.40782127274	-0.00806240163723	0.0582270742502	-0.00167190778706	-0.0497216234914	0.0264762819954	0.010905042378	-0.0552113552738	-0.0506839592384	-0.0287319471681	0.127768764047	-0.00087295525044	-0.00382557017005	0.134528569231	-0.00198194728911	0.165269327647	7.08418748428	-11.5227190535	-17.1635244496
11	4.98899480675	4.98332324961	-2.71712534751	6.52014750345	-3.09220883425	3.20569544891	0.342920274621	-0.371317697648	0.442670350371	0.759104030493	-0.242191042896	0.41907455369	-0.530651728917	0.189310586391	-0.11387133371	0.37268157282	0.0364431995686	0.0270701102814	0.16222229089	-0.0542989092018	0.253154898292	8.33551858987	4.20745857793	-8.44548891488
12	2.79832606839	1.63823170115	-2.62624495732	2.4530146733	-0.504006481034	2.99335689387	-0.178871746029	-0.153909186164	-0.363504236513	-0.104285552595	0.015873267262	-0.466420641355	0.16885202652	0.471534008921	0.135242887641	0.177402462189	0.0045152234563	-0.0373588568014	0.242312756112	0.0114421866206	0.228551829273	19.0150936379	-19.5745873381	-10.0911555496

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 40 )	A	A	1 - 40	1 - 42
2	2	chain 'A' and (resid 41 through 88 )	A	A	41 - 88	43 - 91
3	3	chain 'A' and (resid 89 through 112 )	A	A	89 - 112	92 - 115
4	4	chain 'A' and (resid 113 through 210 )	A	A	113 - 210	116 - 218
5	5	chain 'A' and (resid 211 through 260 )	A	A	211 - 260	219 - 270
6	6	chain 'A' and (resid 261 through 299 )	A	A	261 - 299	271 - 311
7	7	chain 'B' and (resid 1 through 40 )	B	D	1 - 40	1 - 40
8	8	chain 'B' and (resid 41 through 88 )	B	D	41 - 88	41 - 91
9	9	chain 'B' and (resid 89 through 112 )	B	D	89 - 112	92 - 116
10	10	chain 'B' and (resid 113 through 225 )	B	D	113 - 225	117 - 232
11	11	chain 'B' and (resid 226 through 260 )	B	D	226 - 260	233 - 267
12	12	chain 'B' and (resid 261 through 299 )	B	D	261 - 299	268 - 310

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Protein , 1 types, 2 molecules AB

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Sugars , 2 types, 3 molecules

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Non-polymers , 3 types, 329 molecules

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Sample preparation

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-Protein , 1 types, 2 molecules AB

-Sugars , 2 types, 3 molecules

-Non-polymers , 3 types, 329 molecules

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-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

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

-Aug 12, 2020. Covid-19 info

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Components

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Protein , 1 types, 2 molecules AB

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Sugars , 2 types, 3 molecules

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Non-polymers , 3 types, 329 molecules

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Details

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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

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