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

ID or keywords:

Entry

Database: PDB / ID: 9iyh

Title

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.25 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: 2.25 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 2.25 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: 8I8L
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9iyh.cif.gz	215.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9iyh.ent.gz	172.1 KB	Display	PDB format
PDBx/mmJSON format	9iyh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9iyh_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	9iyh_full_validation.pdf.gz	2.5 MB	Display
Data in XML	9iyh_validation.xml.gz	43.3 KB	Display
Data in CIF	9iyh_validation.cif.gz	60.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iy/9iyh ftp://data.pdbj.org/pub/pdb/validation_reports/iy/9iyh	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)	137.925, 78.622, 106.985
Angle α, β, γ (deg.)	90.000, 93.118, 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) / Strain: coaD / 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.: 518 / 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: 2.71 Å³/Da / Density % sol: 54.72 %
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: 2.25→42.668 Å / Num. obs: 52114 / % possible obs: 96.3 % / Redundancy: 2.1 % / CC_1/2: 0.98 / R_merge(I) obs: 0.134 / R_pim(I) all: 0.133 / Net I/σ(I): 4.6
Reflection shell	Resolution: 2.25→2.32 Å / R_merge(I) obs: 0.722 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4601 / CC_1/2: 0.445 / R_pim(I) all: 0.721

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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: 2.25→42.668 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.912 / Cross valid method: FREE R-VALUE / ESU R: 0.354 / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2513	1057	2.03 %
R_work	0.225	51016	-
all	0.226	-	-
obs	-	52073	95.745 %

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: 42.291 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.301 Å²	-0 Å²	0.507 Å²
2-	-	1.116 Å²	0 Å²
3-	-	-	-2.458 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→42.668 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7662	0	68	518	8248

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	7962
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	7655
X-RAY DIFFRACTION	r_angle_refined_deg	1.382	1.827	10770
X-RAY DIFFRACTION	r_angle_other_deg	0.747	1.746	17629
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.879	5	994
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.784	5	51
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.215	10	1399
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.214	10	342
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1223
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	9219
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1769
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1691
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	7128
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	3882
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	3955
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	446
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.045	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.221	0.2	55
X-RAY DIFFRACTION	r_nbd_other	0.3	0.2	210
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.243	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	3.688	4.239	3955
X-RAY DIFFRACTION	r_mcbond_other	3.688	4.239	3955
X-RAY DIFFRACTION	r_mcangle_it	5.8	7.597	4944
X-RAY DIFFRACTION	r_mcangle_other	5.8	7.598	4945
X-RAY DIFFRACTION	r_scbond_it	4.269	4.784	4007
X-RAY DIFFRACTION	r_scbond_other	4.269	4.785	4008
X-RAY DIFFRACTION	r_scangle_it	6.846	8.553	5822
X-RAY DIFFRACTION	r_scangle_other	6.846	8.553	5823
X-RAY DIFFRACTION	r_lrange_it	11.56	52.094	35827
X-RAY DIFFRACTION	r_lrange_other	11.561	52.099	35806
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.093	0.05	4949
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.122	0.05	4869
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.105	0.05	4945
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.083	0.05	5026
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.094	0.05	4939
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.111	0.05	4885
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.099	0.05	4997
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.105	0.05	4920
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.076	0.05	5394
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.127	0.05	4825
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.12	0.05	4835
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.109	0.05	4812
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.114	0.05	4869
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.092	0.05	4926
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.108	0.05	4884

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	0.09264	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09264	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12241	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.12241	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10487	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10487	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08339	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08339	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09424	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.09424	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.11131	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.11131	0.05008
7	13	A	X-RAY DIFFRACTION	Local ncs	0.09903	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.09903	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.10495	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.10495	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.07601	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.07601	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.12659	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.12659	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.12015	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.12015	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.10926	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.10926	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.11416	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.11416	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.09204	0.05009
14	28	A	X-RAY DIFFRACTION	Local ncs	0.09204	0.05009
15	29	A	X-RAY DIFFRACTION	Local ncs	0.10811	0.05008
15	30	A	X-RAY DIFFRACTION	Local ncs	0.10811	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
2.25-2.308	0.356	74	0.334	3814	0.334	3976	0.915	0.925	97.7867	0.332
2.308-2.371	0.351	74	0.325	3729	0.325	3891	0.92	0.929	97.7384	0.32
2.371-2.44	0.367	62	0.295	3603	0.297	3769	0.902	0.94	97.2406	0.289
2.44-2.515	0.317	54	0.296	3535	0.297	3682	0.928	0.942	97.4742	0.289
2.515-2.597	0.308	75	0.279	3401	0.28	3566	0.943	0.95	97.4762	0.27
2.597-2.688	0.269	62	0.254	3255	0.254	3434	0.959	0.957	96.5929	0.243
2.688-2.789	0.228	72	0.233	3159	0.233	3349	0.968	0.965	96.4766	0.221
2.789-2.902	0.268	63	0.218	3017	0.219	3222	0.954	0.969	95.5928	0.21
2.902-3.03	0.247	59	0.233	2891	0.234	3085	0.963	0.966	95.624	0.228
3.03-3.178	0.239	65	0.232	2770	0.232	2961	0.965	0.968	95.7447	0.226
3.178-3.348	0.262	52	0.233	2616	0.234	2775	0.961	0.969	96.1441	0.23
3.348-3.55	0.254	46	0.229	2489	0.23	2641	0.959	0.972	95.9864	0.227
3.55-3.793	0.216	70	0.202	2358	0.202	2536	0.97	0.976	95.7413	0.202
3.793-4.095	0.252	41	0.195	2151	0.196	2310	0.945	0.975	94.8918	0.198
4.095-4.481	0.231	29	0.172	1989	0.173	2154	0.963	0.981	93.6862	0.179
4.481-5.003	0.167	36	0.161	1800	0.161	1967	0.984	0.984	93.3401	0.169
5.003-5.764	0.224	48	0.208	1518	0.208	1724	0.976	0.979	90.8353	0.217
5.764-7.028	0.274	37	0.222	1324	0.223	1477	0.975	0.977	92.1462	0.234
7.028-9.807	0.216	21	0.166	1033	0.167	1170	0.976	0.986	90.0855	0.19
9.807-42.668	0.245	17	0.222	564	0.223	689	0.973	0.966	84.3251	0.247

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