PDB-7bcz: Structure of the 4'-phosphopantetheinyl transferase PcpS from Pse...

ID or keywords:

Entry

Database: PDB / ID: 7bcz

Title

Structure of the 4'-phosphopantetheinyl transferase PcpS from Pseudomonas aeruginosa

Components

4'-phosphopantetheinyl transferase EntD

Keywords

TRANSFERASE / Pseudomonas aeruginosa

Function / homology

COENZYME A / :

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Carivenc, C. / Mourey, L. / Pedelacq, J.D.

Funding support

France, 1items

Citation

Journal: Sci Rep / Year: 2021
Title: Phosphopantetheinyl transferase binding and inhibition by amidino-urea and hydroxypyrimidinethione compounds.
Authors: Carivenc, C. / Maveyraud, L. / Blanger, C. / Ballereau, S. / Roy-Camille, C. / Nguyen, M.C. / Genisson, Y. / Guilhot, C. / Chalut, C. / Pedelacq, J.D. / Mourey, L.

History

Deposition	Dec 21, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7bcz.cif.gz	390.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7bcz.ent.gz	322.6 KB	Display	PDB format
PDBx/mmJSON format	7bcz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7bcz_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7bcz_full_validation.pdf.gz	1.8 MB	Display
Data in XML	7bcz_validation.xml.gz	20.7 KB	Display
Data in CIF	7bcz_validation.cif.gz	31.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bc/7bcz ftp://data.pdbj.org/pub/pdb/validation_reports/bc/7bcz	HTTPS FTP

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Related structure data

Related structure data	7b4rC 7b4sC 7bdwC 6qyfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3phg-1 7bcz-4 3phh-d 3orz-3 5os6-d 4fpx-1 3b1w-4 3a61-d 5dn3-d 2np8-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: 4'-phosphopantetheinyl transferase EntD

B: 4'-phosphopantetheinyl transferase EntD

C: 4'-phosphopantetheinyl transferase EntD

D: 4'-phosphopantetheinyl transferase EntD

hetero molecules

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 4'-phosphopantetheinyl transferase EntD

hetero molecules

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

2

B: 4'-phosphopantetheinyl transferase EntD

hetero molecules

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

3

C: 4'-phosphopantetheinyl transferase EntD

hetero molecules

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

4

D: 4'-phosphopantetheinyl transferase EntD

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.359, 78.872, 81.123
Angle α, β, γ (deg.)	85.62, 84.62, 73.86
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

#1: Protein	4'-phosphopantetheinyl transferase EntD / Enterobactin synthase component D / Enterochelin synthase D Mass: 27031.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: EM867_30290, HAP34_19570, HP562_05455 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6N0ZM94
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.4 Å³/Da / Density % sol: 48.68 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M Na Citrate 10 % PEG4000 10% propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97907 Å / Relative weight: 1
Reflection	Resolution: 2.4→42.49 Å / Num. obs: 39884 / % possible obs: 97.08 % / Redundancy: 5.3 % / B_iso Wilson estimate: 39.33 Å² / CC_1/2: 0.994 / Net I/σ(I): 9.39
Reflection shell	Resolution: 2.4→2.486 Å / Num. unique obs: 3949 / CC_1/2: 0.784

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6QYF

6qyf

Resolution: 2.4→42.49 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2619	3080	3.88 %
R_work	0.2096	-	-
obs	0.2117	39857	96.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→42.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7477	0	194	161	7832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7873
X-RAY DIFFRACTION	f_angle_d	0.724	10729
X-RAY DIFFRACTION	f_dihedral_angle_d	18.683	2851
X-RAY DIFFRACTION	f_chiral_restr	0.041	1170
X-RAY DIFFRACTION	f_plane_restr	0.005	1383

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 (%)
2.4-2.44	0.3436	140	0.2992	3396	X-RAY DIFFRACTION	96
2.44-2.48	0.3655	139	0.2835	3510	X-RAY DIFFRACTION	96
2.48-2.52	0.3106	140	0.2755	3397	X-RAY DIFFRACTION	96
2.52-2.57	0.294	150	0.2815	3416	X-RAY DIFFRACTION	96
2.57-2.62	0.3052	124	0.2828	3547	X-RAY DIFFRACTION	96
2.62-2.67	0.3279	146	0.272	3321	X-RAY DIFFRACTION	95
2.67-2.73	0.3182	131	0.2713	3508	X-RAY DIFFRACTION	96
2.73-2.79	0.2831	135	0.2625	3516	X-RAY DIFFRACTION	97
2.79-2.86	0.298	137	0.2361	3400	X-RAY DIFFRACTION	97
2.86-2.94	0.3017	144	0.2527	3555	X-RAY DIFFRACTION	97
2.94-3.02	0.2656	141	0.2496	3402	X-RAY DIFFRACTION	97
3.02-3.12	0.2611	145	0.2344	3484	X-RAY DIFFRACTION	97
3.12-3.23	0.3456	139	0.2356	3461	X-RAY DIFFRACTION	97
3.23-3.36	0.2897	149	0.2206	3527	X-RAY DIFFRACTION	97
3.36-3.52	0.302	140	0.2127	3447	X-RAY DIFFRACTION	97
3.52-3.7	0.2814	135	0.2073	3501	X-RAY DIFFRACTION	97
3.7-3.93	0.2325	138	0.1844	3436	X-RAY DIFFRACTION	97
3.93-4.23	0.2354	146	0.1717	3541	X-RAY DIFFRACTION	98
4.24-4.66	0.1833	135	0.1581	3485	X-RAY DIFFRACTION	97
4.66-5.33	0.2211	148	0.1598	3483	X-RAY DIFFRACTION	97
5.33-6.72	0.2675	138	0.1963	3462	X-RAY DIFFRACTION	97
6.72-42.49	0.2064	140	0.1734	3502	X-RAY DIFFRACTION	97

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	2.3616	-0.2399	-1.1682	0.4522	0.5328	0.9673	-0.0555	0.2479	-0.4987	0.2533	-0.1146	-0.2687	-0.0202	0.1334	0.1486	0.1968	-0.0836	0.0168	0.3774	-0.0077	0.3238	59.886	15.082	-20.396
2	3.1861	0.5189	0.4155	4.2012	-0.7608	4.6939	-0.0497	-0.3856	-0.0495	0.8294	0.1607	-0.3404	0.3366	0.117	-0.0574	0.4317	0.0763	-0.0445	0.2601	-0.0352	0.2696	61.824	17.58	-10.18
3	2.7181	1.5903	0.4219	4.5439	-0.3569	4.6995	0.1106	-0.7968	0.3569	0.284	-0.0002	-0.2716	-0.24	0.2033	-0.2275	0.302	-0.0552	0.0481	0.2334	-0.1061	0.53	58.42	31.528	-14.28
4	5.4552	4.9043	-3.6634	9.3091	-1.5342	7.6962	-0.6961	-1.2089	-0.371	0.123	0.0228	1.334	0.8699	-0.0576	0.5989	0.6338	-0.1408	0.2652	0.6227	-0.2316	0.7481	42.02	38.208	-1.914
5	6.1533	-1.1656	-1.1069	6.4573	0.513	3.2281	0.2166	-0.0355	0.6336	0.4808	-0.0618	0.1591	-0.1952	0.0107	-0.0898	0.3033	-0.0095	0.045	0.2364	0.0113	0.3106	54.538	41.133	-11.528
6	2.2839	-0.3508	0.4449	5.7488	-0.1169	2.4802	0.017	0.116	0.1871	-0.1313	-0.1536	-0.0304	0.1237	-0.0641	0.126	0.1538	-0.0249	0.0384	0.3026	0.0278	0.2013	43.066	6.282	-30.371
7	3.5576	0.0679	-1.9414	4.5464	-1.1954	3.8205	-0.0266	-0.0875	0.0184	0.4633	0.0621	0.4346	0.1439	-0.0503	-0.0485	0.2884	-0.0297	0.0526	0.2783	-0.015	0.2989	33.383	-9.748	-16.186
8	1.7639	-0.0464	-0.9689	5.3839	-1.3413	3.0066	0.0135	-0.124	-0.0324	0.1524	-0.0963	0.2708	0.0076	-0.1893	0.0436	0.173	-0.0137	-0.0293	0.2994	-0.0477	0.3222	31.268	38.574	37.59
9	2.9215	-0.8448	1.495	4.7449	-0.915	3.1643	0.0256	0.1341	0.0011	-0.4902	-0.0306	0.3414	0.031	-0.0007	-0.0233	0.2849	-0.0205	-0.0085	0.22	0.008	0.2703	21.448	54.69	23.76
10	1.6791	-0.4945	0.268	0.2481	-0.0859	0.0444	-0.3761	0.1236	1.0207	-0.1357	0.1562	-0.9091	0.0243	0.3856	0.1522	0.6261	0.0101	0.031	0.4563	-0.0231	0.9034	50.452	38.37	24.115
11	4.3193	-0.3459	0.5911	3.3166	-0.3102	2.7999	0.1466	0.2771	0.4624	-0.7401	0.0985	-0.2541	-0.2796	0.1611	-0.1614	0.5181	-0.0512	0.0962	0.2787	-0.0483	0.3243	47.753	28.33	19.441
12	3.0406	-1.9481	-0.2905	3.7397	-1.0123	4.5583	0.2381	0.2855	0.3014	-0.7494	-0.4198	-1.1509	-0.5029	0.7737	0.1559	0.5862	-0.1367	0.1898	0.4262	-0.0301	0.5848	56.628	21.92	16.901
13	4.0305	-0.3266	0.898	7.5875	0.9882	3.7051	-0.0121	0.0209	0.4952	-0.4393	-0.1307	-0.4839	0.0919	0.146	-0.0016	0.2625	-0.1097	0.0876	0.2718	-0.1008	0.3974	49.532	17.241	22.97
14	2.84	0.1925	2.6843	4.5031	2.3351	3.561	0.1989	0.6184	0.3446	-1.57	-0.6448	1.631	0.0063	-0.611	0.1156	0.6842	-0.0259	-0.2573	0.595	-0.0623	0.7032	30.782	8.767	11.029
15	4.1028	-0.7204	0.6045	5.6243	0.8384	3.3095	0.2742	-0.0139	-0.1586	-0.6303	-0.089	0.6419	0.0622	-0.0208	-0.1925	0.3992	-0.0347	-0.0675	0.2411	0.0063	0.2639	42.888	3.85	18.976

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 3:30 )	A	3 - 30
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 31:122 )	A	31 - 122
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 123:138 )	A	123 - 138
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 139:149 )	A	139 - 149
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 150:241 )	A	150 - 241
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 6:127 )	B	6 - 127
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 128:241 )	B	128 - 241
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 7:127 )	C	7 - 127
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 128:241 )	C	128 - 241
10	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 3:18 )	D	3 - 18
11	X-RAY DIFFRACTION	11	( CHAIN D AND RESID 19:85 )	D	19 - 85
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 86:111 )	D	86 - 111
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 112:133 )	D	112 - 133
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 134:149 )	D	134 - 149
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 150:241 )	D	150 - 241

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