PDB-6ott: Structure of PurF in complex with ppApp

ID or keywords:

Entry

Database: PDB / ID: 6ott

Title

Structure of PurF in complex with ppApp

Components

Amidophosphoribosyltransferase, PurF

Keywords

cytosolic protein / transferase / complex with ppApp

Function / homology

Function and homology information

amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.55 Å

Authors

Grant, R.A. / Wang, B. / Laub, M.T.

Funding support

United States, 2items

Citation

Journal: Nature / Year: 2019
Title: An interbacterial toxin inhibits target cell growth by synthesizing (p)ppApp.
Authors: Ahmad, S. / Wang, B. / Walker, M.D. / Tran, H.R. / Stogios, P.J. / Savchenko, A. / Grant, R.A. / McArthur, A.G. / Laub, M.T. / Whitney, J.C.

History

Deposition	May 3, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2	Dec 11, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ott.cif.gz	569.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6ott.ent.gz	483.2 KB	Display	PDB format
PDBx/mmJSON format	6ott.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ott_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6ott_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6ott_validation.xml.gz	34.4 KB	Display
Data in CIF	6ott_validation.cif.gz	45.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/6ott ftp://data.pdbj.org/pub/pdb/validation_reports/ot/6ott	HTTPS FTP

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Related structure data

Related structure data	6ox6C 6czf C: citing same article (ref.)
Similar structure data	6czf-d 1ecg-1 1ecj-d 1ecf-1 10890 1ecc-1 5t5v-d 3cc1-1 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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (4) #166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Amidophosphoribosyltransferase, PurF

B: Amidophosphoribosyltransferase, PurF

hetero molecules

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

1

A: Amidophosphoribosyltransferase, PurF

B: Amidophosphoribosyltransferase, PurF

hetero molecules

A: Amidophosphoribosyltransferase, PurF

B: Amidophosphoribosyltransferase, PurF

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.230, 156.830, 107.480
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
1	2	chain A
2	2	chain B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A	A	1 - 496
2	2	1	chain B	B	1 - 496
1	1	2	chain C	A - C	501 - 502
2	2	2	chain D	B - D	501 - 502

NCS ensembles :

ID
1
2

#1: Protein	Amidophosphoribosyltransferase, PurF / ATase / Glutamine phosphoribosylpyrophosphate amidotransferase / GPATase Mass: 56422.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: purF, b2312, JW2309 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG16, amidophosphoribosyltransferase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-N7Y / adenosine 3',5'-bis(trihydrogen diphosphate) Mass: 587.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₅O₁₆P₄ / Feature type: SUBJECT OF INVESTIGATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.83 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Well buffer: 0.1 M HEPES 7.5, 22% PEG-3350, 4% isopropanol Protein: PurF (25mg/mL) with 5 mM ppApp and 10 mM MgCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.55→47.607 Å / Num. obs: 32044 / % possible obs: 99.8 % / Redundancy: 5.812 % / B_iso Wilson estimate: 74.425 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.106 / R_rim(I) all: 0.117 / Χ²: 1.05 / Net I/σ(I): 8.98 / Num. measured all: 186253

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.55-2.62	6.182	1.27	1.01	14491	2345	2344	0.523	1.388	100
2.62-2.69	6.135	1.083	1.22	13982	2279	2279	0.64	1.184	100
2.69-2.77	5.969	0.906	1.59	13286	2228	2226	0.658	0.994	99.9
2.77-2.85	5.731	0.758	1.97	12345	2159	2154	0.778	0.835	99.8
2.85-2.94	5.42	0.65	2.42	11311	2087	2087	0.823	0.721	100
2.94-3.05	6.146	0.494	3.49	12501	2034	2034	0.916	0.541	100
3.05-3.16	6.08	0.362	4.92	11886	1956	1955	0.949	0.397	99.9
3.16-3.29	6.011	0.272	6.23	11354	1890	1889	0.973	0.298	99.9
3.29-3.44	5.857	0.202	8.18	10602	1811	1810	0.986	0.222	99.9
3.44-3.61	5.78	0.153	10.25	10092	1749	1746	0.989	0.169	99.8
3.61-3.8	5.712	0.137	11.3	9413	1649	1648	0.991	0.151	99.9
3.8-4.03	5.417	0.107	13.68	8596	1589	1587	0.993	0.119	99.9
4.03-4.31	4.844	0.092	15.4	6971	1457	1439	0.992	0.104	98.8
4.31-4.66	5.756	0.08	19.54	8081	1404	1404	0.994	0.087	100
4.66-5.1	5.95	0.072	20.49	7556	1271	1270	0.996	0.079	99.9
5.1-5.7	5.935	0.075	20.27	6831	1152	1151	0.995	0.083	99.9
5.7-6.58	5.812	0.068	19.99	6050	1042	1041	0.997	0.075	99.9
6.58-8.06	5.429	0.058	21.82	4750	878	875	0.997	0.064	99.7
8.06-11.4	5.602	0.041	26.34	3899	698	696	0.999	0.045	99.7
11.4-47.607	5.516	0.045	27.11	2256	416	409	0.997	0.05	98.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	5.35 Å	47.61 Å
Translation	5.35 Å	47.61 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.2	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→47.607 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2614	1995	6.23 %
R_work	0.2228	30028	-
obs	0.2252	32023	99.8 %

Solvent computation

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

Displacement parameters

B_iso max: 291 Å² / B_iso mean: 92.1599 Å² / B_iso min: 47.34 Å²

Refinement step

Cycle: final / Resolution: 2.55→47.607 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7798	0	94	0	7892
B_iso mean	-	-	66.62	-	-
Num. residues	-	-	-	-	992

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4873	X-RAY DIFFRACTION	4.087	TORSIONAL
1	2	B	4873	X-RAY DIFFRACTION	4.087	TORSIONAL
2	1	A	50	X-RAY DIFFRACTION	4.087	TORSIONAL
2	2	B	50	X-RAY DIFFRACTION	4.087	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5501-2.6138	0.4104	140	0.3715	2116	2256	100
2.6138-2.6845	0.4142	141	0.3534	2127	2268	100
2.6845-2.7635	0.353	140	0.3409	2107	2247	100
2.7635-2.8527	0.3513	141	0.3347	2123	2264	100
2.8527-2.9546	0.3612	142	0.3178	2139	2281	100
2.9546-3.0729	0.4173	139	0.3125	2113	2252	100
3.0729-3.2127	0.3682	142	0.31	2125	2267	100
3.2127-3.3821	0.3515	142	0.3014	2131	2273	100
3.3821-3.5939	0.2723	143	0.2489	2146	2289	100
3.5939-3.8713	0.254	142	0.2347	2137	2279	100
3.8713-4.2606	0.2176	144	0.2021	2143	2287	99
4.2606-4.8766	0.1963	143	0.161	2162	2305	100
4.8766-6.1419	0.2562	144	0.1911	2177	2321	100
6.1419-47.6148	0.1999	152	0.1675	2282	2434	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	1.7683	0.01	0.7719	1.7067	-0.0406	0.8269	-0.0864	0.0059	0.1278	-0.2451	0.2561	-0.1462	-0.43	-0.082	-0	0.5476	0.008	-0.0351	0.648	0.0023	0.6891	44.0041	25.1768	-24.8284
2	2.1971	-0.7797	-0.5183	1.7947	-0.0126	1.1202	-0.1019	-0.0275	-0.2035	0.0103	0.0015	-0.0138	0.0845	-0.1968	-0	0.5549	-0.0243	-0.0119	0.6127	0.0113	0.6619	43.2623	10.073	-19.0862
3	0.3326	-0.3328	-0.3819	2.5003	1.4499	1.7427	0.007	-0.134	-0.0144	0.1675	-0.0546	0.1576	-0.0464	-0.436	0	0.6242	0.0579	0.0686	0.7984	0.0434	0.7331	32.5192	29.4368	4.7103
4	0.6731	-0.368	0.292	0.803	-0.0241	0.7986	-0.0557	0.0339	0.544	0.282	0.3255	-0.6424	-0.3972	0.379	-0	0.9562	0.0308	0.0204	0.9373	-0.1011	0.9334	48.4568	43.3587	4.3017
5	0.9349	-0.6165	-0.104	2.5419	0.7568	2.3708	-0.1464	-0.0324	-0.0689	0.2768	0.2014	-0.1821	0.0317	0.1275	-0	0.7368	0.0185	0.0405	0.7796	0.0322	0.6999	42.8958	24.2837	10.0925
6	0.2047	0.2005	-0.0899	0.0674	-0.1042	-0.016	0.2105	0.7554	-0.7848	0.6746	-0.1524	-0.6276	-1.0989	0.6255	-0.0002	1.3424	-0.2184	-0.1506	1.5161	0.0856	1.4962	62.9904	22.129	-5.5282
7	0.664	0.323	0.0384	1.8025	-0.2987	1.8132	-0.4767	0.0604	-0.4372	-0.3805	0.3278	-0.3267	-0.371	0.0285	0	0.8855	-0.0687	0.058	0.6805	-0.0587	0.7942	54.2259	53.8398	-13.2337
8	2.629	0.1845	-0.1357	2.9843	-1.1146	2.8811	0.2137	-0.055	0.2695	-0.2757	-0.0071	0.0337	-0.8422	-0.1921	-0	1.325	0.0721	0.1425	0.6012	-0.0453	0.7045	49.2431	70.1706	-19.2352
9	1.8117	1.3453	-0.3195	1.6396	0.2853	1.2149	0.2735	-0.2454	0.1638	0.2014	-0.1369	0.1722	-0.6391	-0.1996	0	0.9892	0.1659	0.0755	0.8163	-0.0207	0.669	36.2367	59.4257	-2.321
10	1.4888	-0.357	-0.0293	1.4596	-0.4678	0.7431	0.0568	0.371	0.1629	-0.2702	0.0062	0.0291	0.1901	-0.347	-0	0.7444	0.0609	-0.0073	0.9204	-0.0148	0.8074	26.112	35.2315	-13.5075
11	1.0631	-0.2348	0.6851	1.4382	-0.49	1.9617	-0.0653	0.2026	0.108	-0.2248	0.2285	0.2727	-0.678	-0.6103	0	0.8226	0.2786	0.0531	1.0261	-0.009	0.8421	19.7554	53.841	-14.4651
12	0.0232	0.0671	0.0422	0.1627	0.134	-0.0938	0.2793	0.4711	-0.9571	-0.5471	-0.1506	1.1054	-0.1068	1.4699	0.0002	1.5562	0.4069	-0.347	1.664	-0.1902	1.5264	36.8973	56.7545	-33.6944

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 1 through 62 )	A	1 - 62
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 242 )	A	63 - 242
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 243 through 331 )	A	243 - 331
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 332 through 372 )	A	332 - 372
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 373 through 471 )	A	373 - 471
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 472 through 496 )	A	472 - 496
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 60 )	B	1 - 60
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 61 through 182 )	B	61 - 182
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 183 through 305 )	B	183 - 305
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 306 through 361 )	B	306 - 361
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 362 through 471 )	B	362 - 471
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 472 through 496 )	B	472 - 496

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