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

ID or keywords:

Entry

Database: PDB / ID: 9iyf

Title

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.37 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: 2.37 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 expression tag bound in the substrate binding site of a neighbouring molecule at 2.37 A resolution.
Authors: Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.

History

Deposition	Jul 30, 2024	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Aug 21, 2024	ID: 8I8N
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9iyf.cif.gz	216.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9iyf.ent.gz	172.7 KB	Display	PDB format
PDBx/mmJSON format	9iyf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iy/9iyf ftp://data.pdbj.org/pub/pdb/validation_reports/iy/9iyf	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

116 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
Evidence: gel filtration
38.7 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
38.8 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
38.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	137.268, 78.418, 106.465
Angle α, β, γ (deg.)	90.000, 93.100, 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	15 - 172
2	1	1	LEU	LEU	1 - 158	15 - 172
3	2	2	LYS	LYS	1 - 159	15 - 173
4	2	2	LYS	LYS	1 - 159	15 - 173
5	3	3	LYS	LYS	1 - 159	15 - 173
6	3	3	LYS	LYS	1 - 159	15 - 173
7	4	4	LYS	LYS	1 - 159	15 - 173
8	4	4	LYS	LYS	1 - 159	15 - 173
9	5	5	LEU	LEU	1 - 158	15 - 172
10	5	5	LEU	LEU	1 - 158	15 - 172
11	6	6	LEU	LEU	1 - 158	15 - 172
12	6	6	LEU	LEU	1 - 158	15 - 172
13	7	7	LEU	LEU	1 - 158	15 - 172
14	7	7	LEU	LEU	1 - 158	15 - 172
15	8	8	LEU	LEU	1 - 158	15 - 172
16	8	8	LEU	LEU	1 - 158	15 - 172
17	9	9	LYS	LYS	1 - 159	15 - 173
18	9	9	LYS	LYS	1 - 159	15 - 173
19	10	10	LYS	LYS	1 - 159	15 - 173
20	10	10	LYS	LYS	1 - 159	15 - 173
21	11	11	LYS	LYS	1 - 159	15 - 173
22	11	11	LYS	LYS	1 - 159	15 - 173
23	12	12	LEU	LEU	1 - 158	15 - 172
24	12	12	LEU	LEU	1 - 158	15 - 172
25	13	13	LYS	LYS	1 - 159	15 - 173
26	13	13	LYS	LYS	1 - 159	15 - 173
27	14	14	LEU	LEU	1 - 158	15 - 172
28	14	14	LEU	LEU	1 - 158	15 - 172
29	15	15	LEU	LEU	1 - 158	15 - 172
30	15	15	LEU	LEU	1 - 158	15 - 172

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: 19182.268 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-PAE / PHOSPHONOACETIC ACID Mass: 140.032 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₅O₅P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.68 Å³/Da / Density % sol: 54.16 %
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: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 2.37→42.486 Å / Num. obs: 43453 / % possible obs: 94.9 % / Redundancy: 2.1 % / CC_1/2: 0.964 / R_merge(I) obs: 0.233 / R_pim(I) all: 0.233 / Net I/σ(I): 2.6
Reflection shell	Resolution: 2.37→2.46 Å / Redundancy: 2.1 % / R_merge(I) obs: 1.235 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4673 / CC_1/2: 0.34 / R_pim(I) all: 1.234 / % possible all: 97.4

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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: 2.37→42.486 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.904 / WR_factor R_free: 0.249 / WR_factor R_work: 0.22 / Average fsc free: 0.9446 / Average fsc work: 0.9518 / Cross valid method: FREE R-VALUE / ESU R: 0.511 / ESU R Free: 0.266
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2464	863	1.986 %
R_work	0.2197	42590	-
all	0.22	-	-
obs	-	43453	94.377 %

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: 44.031 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.857 Å²	0 Å²	0.133 Å²
2-	-	0.74 Å²	0 Å²
3-	-	-	-2.596 Å²

Refinement step

Cycle: LAST / Resolution: 2.37→42.486 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7662	0	68	573	8303

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	7946
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	7641
X-RAY DIFFRACTION	r_angle_refined_deg	1.317	1.826	10747
X-RAY DIFFRACTION	r_angle_other_deg	0.72	1.745	17597
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.956	5	992
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.875	5	50
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.527	10	1396
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.499	10	341
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1221
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	9197
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1763
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	1738
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	7264
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	3900
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4031
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	446
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.053	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.194	0.2	68
X-RAY DIFFRACTION	r_nbd_other	0.245	0.2	237
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.23	0.2	32
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.069	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.207	4.532	3953
X-RAY DIFFRACTION	r_mcbond_other	3.207	4.532	3953
X-RAY DIFFRACTION	r_mcangle_it	5.355	8.12	4941
X-RAY DIFFRACTION	r_mcangle_other	5.355	8.121	4942
X-RAY DIFFRACTION	r_scbond_it	3.444	5	3993
X-RAY DIFFRACTION	r_scbond_other	3.444	5	3994
X-RAY DIFFRACTION	r_scangle_it	5.855	8.993	5803
X-RAY DIFFRACTION	r_scangle_other	5.854	8.993	5804
X-RAY DIFFRACTION	r_lrange_it	11.445	55.681	36148
X-RAY DIFFRACTION	r_lrange_other	11.447	55.695	36114
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.106	0.05	4966
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.139	0.05	4913
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.116	0.05	4995
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.087	0.05	5091
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.106	0.05	4950
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.131	0.05	4901
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.107	0.05	4999
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.114	0.05	4939
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.09	0.05	5428
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.146	0.05	4853
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.138	0.05	4852
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.131	0.05	4818
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.128	0.05	4877
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.107	0.05	4922
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.116	0.05	4902

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	0.10581	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10581	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13948	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.13948	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11647	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11647	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08715	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08715	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.10634	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.10634	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.13086	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.13086	0.05008
7	13	A	X-RAY DIFFRACTION	Local ncs	0.10736	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.10736	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.11402	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.11402	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.08974	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.08974	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.14649	0.05008
10	20	A	X-RAY DIFFRACTION	Local ncs	0.14649	0.05008
11	21	A	X-RAY DIFFRACTION	Local ncs	0.13805	0.05008
11	22	A	X-RAY DIFFRACTION	Local ncs	0.13805	0.05008
12	23	A	X-RAY DIFFRACTION	Local ncs	0.13135	0.05008
12	24	A	X-RAY DIFFRACTION	Local ncs	0.13135	0.05008
13	25	A	X-RAY DIFFRACTION	Local ncs	0.1278	0.05008
13	26	A	X-RAY DIFFRACTION	Local ncs	0.1278	0.05008
14	27	A	X-RAY DIFFRACTION	Local ncs	0.10702	0.05009
14	28	A	X-RAY DIFFRACTION	Local ncs	0.10702	0.05009
15	29	A	X-RAY DIFFRACTION	Local ncs	0.11558	0.05008
15	30	A	X-RAY DIFFRACTION	Local ncs	0.11558	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
2.37-2.431	0.328	67	0.334	3183	0.334	3352	0.93	0.91	96.957	0.33
2.431-2.498	0.37	65	0.331	3156	0.332	3322	0.884	0.912	96.9597	0.328
2.498-2.57	0.327	75	0.327	2996	0.327	3182	0.922	0.921	96.5116	0.326
2.57-2.649	0.32	75	0.31	2931	0.31	3118	0.927	0.928	96.408	0.303
2.649-2.735	0.291	62	0.282	2813	0.282	3011	0.939	0.941	95.4832	0.276
2.735-2.831	0.279	47	0.267	2771	0.267	2940	0.95	0.947	95.8503	0.259
2.831-2.937	0.284	38	0.25	2650	0.25	2817	0.948	0.954	95.4207	0.244
2.937-3.057	0.303	57	0.257	2509	0.258	2685	0.926	0.95	95.568	0.251
3.057-3.192	0.283	49	0.231	2428	0.232	2601	0.952	0.963	95.2326	0.225
3.192-3.347	0.242	48	0.223	2258	0.223	2487	0.961	0.966	92.7222	0.216
3.347-3.526	0.207	44	0.212	2209	0.212	2385	0.972	0.971	94.4654	0.209
3.526-3.739	0.164	35	0.203	2089	0.202	2265	0.98	0.973	93.7748	0.201
3.739-3.995	0.221	34	0.182	1951	0.183	2120	0.964	0.979	93.6321	0.184
3.995-4.311	0.217	31	0.176	1779	0.177	1954	0.964	0.979	92.6305	0.18
4.311-4.718	0.191	27	0.155	1677	0.155	1840	0.98	0.983	92.6087	0.164
4.718-5.267	0.207	17	0.165	1505	0.166	1662	0.975	0.983	91.5764	0.177
5.267-6.066	0.256	22	0.193	1306	0.194	1461	0.961	0.98	90.8966	0.203
6.066-7.392	0.214	20	0.156	1091	0.157	1244	0.969	0.986	89.3087	0.169
7.392-10.299	0.138	36	0.112	820	0.113	987	0.989	0.991	86.7275	0.129
10.299-42.486	0.238	14	0.194	468	0.195	600	0.961	0.973	80.3333	0.25

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