PDB-9iyg: Structure of Phosphopantetheine adenylyltransferase (PPAT) from E...

ID or keywords:

Entry

Database: PDB / ID: 9iyg

Title

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.60 A resolution.

Components

Phosphopantetheine adenylyltransferase

Keywords

TRANSFERASE / coaD / PPAT / COENZYME A biosynthesis

Function / homology

Function and homology information

pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function

Biological species

Enterobacter sp. 638 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.60 A resolution.
Authors: Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.

History

Deposition	Jul 30, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9iyg.cif.gz	215.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9iyg.ent.gz	171.4 KB	Display	PDB format
PDBx/mmJSON format	9iyg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9iyg_validation.pdf.gz	515.7 KB	Display	wwPDB validaton report
Full document	9iyg_full_validation.pdf.gz	529.4 KB	Display
Data in XML	9iyg_validation.xml.gz	43.5 KB	Display
Data in CIF	9iyg_validation.cif.gz	59.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iy/9iyg ftp://data.pdbj.org/pub/pdb/validation_reports/iy/9iyg	HTTPS FTP

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Related structure data

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

Deposited unit

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

D: Phosphopantetheine adenylyltransferase

E: Phosphopantetheine adenylyltransferase

F: Phosphopantetheine adenylyltransferase

hetero molecules

118 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

hetero molecules

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

2

C: Phosphopantetheine adenylyltransferase

D: Phosphopantetheine adenylyltransferase

hetero molecules

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

3

E: Phosphopantetheine adenylyltransferase

F: Phosphopantetheine adenylyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	138.271, 79.846, 107.541
Angle α, β, γ (deg.)	90.000, 93.354, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	1 - 158	18 - 175
2	1	1	LEU	LEU	1 - 158	18 - 175
3	2	2	LYS	LYS	1 - 159	18 - 176
4	2	2	LYS	LYS	1 - 159	18 - 176
5	3	3	LEU	LEU	1 - 158	18 - 175
6	3	3	LEU	LEU	1 - 158	18 - 175
7	4	4	LYS	LYS	1 - 159	18 - 176
8	4	4	LYS	LYS	1 - 159	18 - 176
9	5	5	LYS	LYS	1 - 159	18 - 176
10	5	5	LYS	LYS	1 - 159	18 - 176
11	6	6	LEU	LEU	1 - 158	18 - 175
12	6	6	LEU	LEU	1 - 158	18 - 175
13	7	7	LYS	LYS	1 - 159	18 - 176
14	7	7	LYS	LYS	1 - 159	18 - 176
15	8	8	LEU	LEU	1 - 158	18 - 175
16	8	8	LEU	LEU	1 - 158	18 - 175
17	9	9	LEU	LEU	1 - 158	18 - 175
18	9	9	LEU	LEU	1 - 158	18 - 175
19	10	10	LEU	LEU	1 - 158	18 - 175
20	10	10	LEU	LEU	1 - 158	18 - 175
21	11	11	LYS	LYS	1 - 159	18 - 176
22	11	11	LYS	LYS	1 - 159	18 - 176
23	12	12	LYS	LYS	1 - 159	18 - 176
24	12	12	LYS	LYS	1 - 159	18 - 176
25	13	13	LEU	LEU	1 - 158	18 - 175
26	13	13	LEU	LEU	1 - 158	18 - 175
27	14	14	LEU	LEU	1 - 158	18 - 175
28	14	14	LEU	LEU	1 - 158	18 - 175
29	15	15	LYS	LYS	1 - 159	18 - 176
30	15	15	LYS	LYS	1 - 159	18 - 176

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT Mass: 19464.545 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. 638 (bacteria) / Gene: coaD, Ent638_0105 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A4W515, pantetheine-phosphate adenylyltransferase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.78 Å³/Da / Density % sol: 55.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 2.6→69.12 Å / Num. obs: 35497 / % possible obs: 98.1 % / Redundancy: 3.3 % / CC_1/2: 0.925 / R_merge(I) obs: 0.167 / R_pim(I) all: 0.162 / Net I/σ(I): 3.8
Reflection shell	Resolution: 2.6→2.72 Å / R_merge(I) obs: 1.059 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3834 / CC_1/2: 0.44 / R_pim(I) all: 1.01 / % possible all: 87.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
MxCuBE		data collection
XDS		data reduction
autoPROC		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→59.736 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.896 / Cross valid method: FREE R-VALUE / ESU R: 1.349 / ESU R Free: 0.348
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2702	699	1.974 %
R_work	0.2271	34714	-
all	0.228	-	-
obs	-	35413	97.815 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.066 Å²	0 Å²	0.314 Å²
2-	-	0.67 Å²	-0 Å²
3-	-	-	-4.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→59.736 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7702	0	84	456	8242

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	7976
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	7660
X-RAY DIFFRACTION	r_angle_refined_deg	1.418	1.821	10785
X-RAY DIFFRACTION	r_angle_other_deg	0.813	1.746	17631
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.91	5	990
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.654	5	51
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.726	10	1398
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.154	10	339
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1219
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9241
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1771
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	1486
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.208	0.2	6471
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	3767
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	3790
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	319
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.141	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	41
X-RAY DIFFRACTION	r_nbd_other	0.225	0.2	153
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.156	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	4.41	5.967	3960
X-RAY DIFFRACTION	r_mcbond_other	4.409	5.968	3960
X-RAY DIFFRACTION	r_mcangle_it	7.114	10.742	4944
X-RAY DIFFRACTION	r_mcangle_other	7.115	10.744	4945
X-RAY DIFFRACTION	r_scbond_it	4.627	6.574	4016
X-RAY DIFFRACTION	r_scbond_other	4.621	6.57	4013
X-RAY DIFFRACTION	r_scangle_it	7.709	11.864	5839
X-RAY DIFFRACTION	r_scangle_other	7.708	11.865	5840
X-RAY DIFFRACTION	r_lrange_it	12.927	72.191	31883
X-RAY DIFFRACTION	r_lrange_other	12.905	72.32	31606
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.089	0.05	4761
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.055	0.05	4961
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.087	0.05	4781
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.079	0.05	4829
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.114	0.05	4661
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.093	0.05	4804
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.083	0.05	5257
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.087	0.05	4796
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.119	0.05	4653
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.089	0.05	4800
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.083	0.05	4837
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.113	0.05	4651
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.091	0.05	4772
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.12	0.05	4621
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.117	0.05	4650

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08932	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08932	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05486	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05486	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08662	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.08662	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0794	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0794	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.11408	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.11408	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09329	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09329	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08261	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08261	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.08721	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.08721	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.11908	0.05008
9	18	A	X-RAY DIFFRACTION	Local ncs	0.11908	0.05008
10	19	A	X-RAY DIFFRACTION	Local ncs	0.08933	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.08933	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.08326	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.08326	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.1133	0.05008
12	24	A	X-RAY DIFFRACTION	Local ncs	0.1133	0.05008
13	25	A	X-RAY DIFFRACTION	Local ncs	0.09127	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.09127	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.11992	0.05009
14	28	A	X-RAY DIFFRACTION	Local ncs	0.11992	0.05009
15	29	A	X-RAY DIFFRACTION	Local ncs	0.11696	0.05008
15	30	A	X-RAY DIFFRACTION	Local ncs	0.11696	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.6-2.667	0.39	33	0.359	2207	0.359	2701	0.893	0.888	82.9322	0.358
2.667-2.74	0.324	52	0.342	2397	0.342	2594	0.928	0.908	94.4102	0.345
2.74-2.82	0.306	49	0.321	2390	0.321	2494	0.929	0.916	97.7947	0.323
2.82-2.906	0.286	40	0.287	2379	0.287	2442	0.917	0.936	99.0582	0.283
2.906-3.001	0.324	33	0.268	2311	0.269	2355	0.95	0.946	99.5329	0.262
3.001-3.106	0.263	27	0.276	2276	0.276	2308	0.936	0.947	99.7834	0.269
3.106-3.223	0.396	42	0.25	2155	0.252	2203	0.896	0.957	99.7276	0.243
3.223-3.354	0.262	45	0.223	2114	0.224	2164	0.945	0.967	99.769	0.217
3.354-3.503	0.272	37	0.237	1982	0.238	2023	0.95	0.965	99.8023	0.232
3.503-3.673	0.3	28	0.281	1910	0.281	1957	0.913	0.933	99.0291	0.271
3.673-3.871	0.294	56	0.274	1769	0.274	1854	0.947	0.939	98.4358	0.264
3.871-4.105	0.281	52	0.212	1723	0.214	1782	0.956	0.972	99.6072	0.209
4.105-4.387	0.286	34	0.184	1623	0.186	1659	0.952	0.977	99.8794	0.186
4.387-4.736	0.197	39	0.161	1518	0.162	1559	0.976	0.984	99.8717	0.166
4.736-5.185	0.272	46	0.158	1380	0.162	1429	0.959	0.984	99.7901	0.165
5.185-5.792	0.254	31	0.189	1272	0.19	1306	0.97	0.979	99.7703	0.196
5.792-6.677	0.246	12	0.203	1151	0.204	1164	0.975	0.976	99.9141	0.208
6.677-8.153	0.208	19	0.168	955	0.168	979	0.982	0.982	99.4893	0.182
8.153-11.424	0.172	17	0.125	757	0.126	774	0.985	0.99	100	0.139
11.424-59.736	0.205	7	0.271	445	0.27	454	0.977	0.938	99.5595	0.395

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