PDB-6b7d: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas...

ID or keywords:

Entry

Database: PDB / ID: 6b7d

Title

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 3-(4-chlorophenyl)-6-methoxy-4,5-dimethylpyridazine

Components

Phosphopantetheine adenylyltransferase

Keywords

TRANSFERASE / CoaD

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Proudfoot, A.W. / Bussiere, D. / Lingel, A.

Citation

Journal: J. Am. Chem. Soc. / Year: 2017
Title: High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization.
Authors: Proudfoot, A. / Bussiere, D.E. / Lingel, A.

History

Deposition	Oct 3, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 27, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6b7d.cif.gz	149 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/6b7d ftp://data.pdbj.org/pub/pdb/validation_reports/b7/6b7d	HTTPS FTP

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Related structure data

Related structure data	6b7aC 6b7bC 6b7cC 6b7eC 6b7fC 5jbnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6b7e-1 6ccm-1 6ckw-1 6cho-1 6chl-1 6b7b-1 6cco-1 1gn8-1 6b7f-1 1b6t-1 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 - FunctionF&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

Deposited unit

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

hetero molecules

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

1

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

hetero molecules

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

hetero molecules

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
117 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Idetical with deposited unit
defined by author&software

3

B: Phosphopantetheine adenylyltransferase

hetero molecules

x 12

A: Phosphopantetheine adenylyltransferase

hetero molecules

x 12

defined by software
467 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_355	-x-2,-y,z	1
crystal symmetry operation	3_357	-x-2,y,-z+2	1
crystal symmetry operation	4_557	x,-y,-z+2	1
crystal symmetry operation	5_366	z-2,x+1,y+1	1
crystal symmetry operation	6_346	z-2,-x-1,-y+1	1
crystal symmetry operation	7_546	-z,-x-1,y+1	1
crystal symmetry operation	8_566	-z,x+1,-y+1	1
crystal symmetry operation	9_447	y-1,z-1,x+2	1
crystal symmetry operation	10_445	-y-1,z-1,-x	1
crystal symmetry operation	11_465	y-1,-z+1,-x	1
crystal symmetry operation	12_467	-y-1,-z+1,x+2	1
crystal symmetry operation	13_444	x-1/2,y-1/2,z-1/2	1
crystal symmetry operation	14_354	-x-3/2,-y+1/2,z-1/2	1
crystal symmetry operation	15_347	-x-3/2,y-1/2,-z+5/2	1
crystal symmetry operation	16_457	x-1/2,-y+1/2,-z+5/2	1
crystal symmetry operation	17_255	z-5/2,x+1/2,y+1/2	1
crystal symmetry operation	18_246	z-5/2,-x-1/2,-y+3/2	1
crystal symmetry operation	19_545	-z+1/2,-x-1/2,y+1/2	1
crystal symmetry operation	20_556	-z+1/2,x+1/2,-y+3/2	1
crystal symmetry operation	21_336	y-3/2,z-3/2,x+3/2	1
crystal symmetry operation	22_435	-y-1/2,z-3/2,-x+1/2	1
crystal symmetry operation	23_365	y-3/2,-z+3/2,-x+1/2	1
crystal symmetry operation	24_466	-y-1/2,-z+3/2,x+3/2	1

4

A: Phosphopantetheine adenylyltransferase

hetero molecules

A: Phosphopantetheine adenylyltransferase

hetero molecules

A: Phosphopantetheine adenylyltransferase

hetero molecules

defined by software
58.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

B: Phosphopantetheine adenylyltransferase

hetero molecules

B: Phosphopantetheine adenylyltransferase

hetero molecules

B: Phosphopantetheine adenylyltransferase

hetero molecules

defined by software
58.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.990, 134.990, 134.990
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	197
Space group name H-M	I23

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 3 through 5 or resid 7...
2	1	(chain B and (resid 3 through 5 or resid 7...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	ALA	ALA	(chain A and (resid 3 through 5 or resid 7...	A	A	3 - 5	3 - 5
1	2	TYR	TYR	GLY	GLY	(chain A and (resid 3 through 5 or resid 7...	A	A	7 - 9	7 - 9
1	3	PHE	PHE	ILE	ILE	(chain A and (resid 3 through 5 or resid 7...	A	A	11 - 19	11 - 19
1	4	VAL	VAL	GLN	GLN	(chain A and (resid 3 through 5 or resid 7...	A	A	22 - 27	22 - 27
1	5	PHE	PHE	PHE	PHE	(chain A and (resid 3 through 5 or resid 7...	A	A	29	29
1	6	HIS	HIS	ILE	ILE	(chain A and (resid 3 through 5 or resid 7...	A	A	31 - 33	31 - 33
1	7	ALA	ALA	PRO	PRO	(chain A and (resid 3 through 5 or resid 7...	A	A	35 - 44	35 - 44
1	8	PHE	PHE	THR	THR	(chain A and (resid 3 through 5 or resid 7...	A	A	46 - 47	46 - 47
1	9	GLU	GLU	VAL	VAL	(chain A and (resid 3 through 5 or resid 7...	A	A	50 - 67	50 - 67
1	10	GLY	GLY	SER	SER	(chain A and (resid 3 through 5 or resid 7...	A	A	69 - 71	69 - 71
1	11	LEU	LEU	ARG	ARG	(chain A and (resid 3 through 5 or resid 7...	A	A	73 - 79	73 - 79
1	12	GLN	GLN	GLU	GLU	(chain A and (resid 3 through 5 or resid 7...	A	A	81 - 99	81 - 99
1	13	ALA	ALA	ARG	ARG	(chain A and (resid 3 through 5 or resid 7...	A	A	103 - 107	103 - 107
1	14	LEU	LEU	PRO	PRO	(chain A and (resid 3 through 5 or resid 7...	A	A	109 - 111	109 - 111
1	15	LEU	LEU	SER	SER	(chain A and (resid 3 through 5 or resid 7...	A	A	113 - 115	113 - 115
1	16	PHE	PHE	PHE	PHE	(chain A and (resid 3 through 5 or resid 7...	A	A	117	117
1	17	PRO	PRO	TRP	TRP	(chain A and (resid 3 through 5 or resid 7...	A	A	120 - 124	120 - 124
1	18	PHE	PHE	SER	SER	(chain A and (resid 3 through 5 or resid 7...	A	A	126 - 129	126 - 129
1	19	LEU	LEU	PRO	PRO	(chain A and (resid 3 through 5 or resid 7...	A	A	131 - 147	131 - 147
1	20	GLU	GLU	GLU	GLU	(chain A and (resid 3 through 5 or resid 7...	A	A	148	148
1	21	MET	MET	VAL	VAL	(chain A and (resid 3 through 5 or resid 7...	A	A	1 - 160	1 - 160
1	22	MET	MET	VAL	VAL	(chain A and (resid 3 through 5 or resid 7...	A	A	1 - 160	1 - 160
1	23	MET	MET	VAL	VAL	(chain A and (resid 3 through 5 or resid 7...	A	A	1 - 160	1 - 160
1	24	MET	MET	VAL	VAL	(chain A and (resid 3 through 5 or resid 7...	A	A	1 - 160	1 - 160
1	25	MET	MET	VAL	VAL	(chain A and (resid 3 through 5 or resid 7...	A	A	1 - 160	1 - 160
2	1	LYS	LYS	ALA	ALA	(chain B and (resid 3 through 5 or resid 7...	B	B	3 - 5	3 - 5
2	2	TYR	TYR	GLY	GLY	(chain B and (resid 3 through 5 or resid 7...	B	B	7 - 9	7 - 9
2	3	PHE	PHE	ILE	ILE	(chain B and (resid 3 through 5 or resid 7...	B	B	11 - 19	11 - 19
2	4	VAL	VAL	GLN	GLN	(chain B and (resid 3 through 5 or resid 7...	B	B	22 - 27	22 - 27
2	5	PHE	PHE	PHE	PHE	(chain B and (resid 3 through 5 or resid 7...	B	B	29	29
2	6	HIS	HIS	ILE	ILE	(chain B and (resid 3 through 5 or resid 7...	B	B	31 - 33	31 - 33
2	7	ALA	ALA	SER	SER	(chain B and (resid 3 through 5 or resid 7...	B	B	35 - 39	35 - 39
2	8	PRO	PRO	PRO	PRO	(chain B and (resid 3 through 5 or resid 7...	B	B	40	40
2	9	GLN	GLN	ALA	ALA	(chain B and (resid 3 through 5 or resid 7...	B	B	2 - 159	2 - 159
2	10	GLN	GLN	ALA	ALA	(chain B and (resid 3 through 5 or resid 7...	B	B	2 - 159	2 - 159
2	11	GLN	GLN	ALA	ALA	(chain B and (resid 3 through 5 or resid 7...	B	B	2 - 159	2 - 159
2	12	GLN	GLN	ALA	ALA	(chain B and (resid 3 through 5 or resid 7...	B	B	2 - 159	2 - 159

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Protein , 1 types, 2 molecules AB

#1: Protein	Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT Mass: 18902.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: coaD, kdtB, yicA, b3634, JW3609 / Production host: Escherichia coli (E. coli) References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase

#1: Protein

Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT

Mass: 18902.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: coaD, kdtB, yicA, b3634, JW3609 / Production host:

Escherichia coli (E. coli)
References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase

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Non-polymers , 5 types, 398 molecules

#2: Chemical	ChemComp-CWG / 3-(4-chlorophenyl)-6-methoxy-4,5-dimethylpyridazine Mass: 248.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₁₃ClN₂O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.49 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.8 M AMMONIUM SULFATE, 0.25 M POTASSIUM THIOCYANATE, 0.2 M POTASSIUM BROMIDE

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 1, 2017

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.8→47.73 Å / Num. obs: 37916 / % possible obs: 100 % / Redundancy: 10.7 % / B_iso Wilson estimate: 22.96 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.023 / R_rim(I) all: 0.075 / Net I/σ(I): 21

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.8-1.84	10.2	0.734	2225	0.882	0.242	0.773	100
9-47.73	9.7	0.019	329	1	0.006	0.02	97.8

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Processing

Software

Name	Version	Classification
Aimless	0.5.27	data scaling
PHENIX	1.12_2829	refinement
PDB_EXTRACT	3.22	data extraction
iMOSFLM	7.2.1	data reduction
PHENIX	1.12_2829	phasing
Coot	0.8.8	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JBN

5jbn

Resolution: 1.8→28.78 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.19

	R_factor	Num. reflection	% reflection
R_free	0.1973	1830	4.83 %
R_work	0.1836	-	-
obs	0.1843	37860	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 93.66 Å² / B_iso mean: 27.4266 Å² / B_iso min: 11.7 Å²

Refinement step

Cycle: final / Resolution: 1.8→28.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2440	0	58	387	2885
B_iso mean	-	-	54.35	41.09	-
Num. residues	-	-	-	-	315

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2673
X-RAY DIFFRACTION	f_angle_d	0.794	3659
X-RAY DIFFRACTION	f_chiral_restr	0.048	415
X-RAY DIFFRACTION	f_plane_restr	0.004	465
X-RAY DIFFRACTION	f_dihedral_angle_d	15.556	1614

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1064	X-RAY DIFFRACTION	10.524	TORSIONAL
1	2	B	1064	X-RAY DIFFRACTION	10.524	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.8003-1.849	0.2723	121	0.2626	2800	2921
1.849-1.9034	0.2737	144	0.2363	2706	2850
1.9034-1.9648	0.2412	102	0.2095	2781	2883
1.9648-2.035	0.2047	153	0.2004	2743	2896
2.035-2.1165	0.2274	141	0.2046	2768	2909
2.1165-2.2128	0.2413	138	0.2042	2762	2900
2.2128-2.3294	0.2258	146	0.1908	2746	2892
2.3294-2.4753	0.2337	125	0.1958	2761	2886
2.4753-2.6663	0.213	136	0.197	2790	2926
2.6663-2.9344	0.2197	143	0.1868	2765	2908
2.9344-3.3584	0.2039	158	0.1782	2768	2926
3.3584-4.2291	0.1691	179	0.1552	2760	2939
4.2291-28.7836	0.1477	144	0.1638	2880	3024

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	-0.0022	-0.0002	0.0019	0.0018	-0.003	-0.0003	-0.0757	0.0112	-0.0428	0.0348	-0.0706	0.0143	-0.0544	-0.0018	-0	0.0406	-0.0695	-0.0447	-0.2269	0.0698	-0.0844	-112.6062	45.2968	190.5975
2	0.0017	0.0007	-0.001	0.0034	-0.0018	0.0022	0.0269	0.0055	-0.0069	0.036	0.0227	-0.002	-0.0248	0.0196	-0	0.1073	0.0073	-0.0083	0.072	-0.0189	0.0745	-108.6468	34.7269	190.4959
3	-0.0014	0.0006	-0.0007	0.0021	-0.0048	0.0033	-0.0028	0.0177	0.0075	0.0212	-0.0031	-0.0253	0.0033	-0.0169	0	0.1492	-0.0266	-0.0233	0.051	0.0154	0.1064	-108.6547	55.6005	179.2837
4	0.0073	-0.0053	0.001	0.0038	-0.0034	0.0008	0.0328	0.0162	-0.076	0.0494	0.0106	0.0108	-0.0213	-0.0366	0	0.0392	-0.0018	-0.0197	0.072	-0.0308	0.1058	-124.4583	19.8544	177.1876
5	0.0003	-0.0012	-0.0003	-0.0003	-0.0006	0.0008	-0.0027	-0.0001	-0.0037	-0.0081	0.0027	-0.0201	0.0026	-0.0049	0	0.1425	-0.0238	-0.002	0.1397	-0.0053	0.1109	-118.2357	34.3583	169.4848
6	0.0023	-0.0087	-0.0046	0.0004	-0.0037	0.0069	-0.007	-0.0062	-0.027	0.0121	0.0023	0.005	-0.0078	0.0114	0	0.0885	0.0132	-0.0059	0.0841	-0.0125	0.1483	-113.1777	13.915	173.8806

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 58 )	A	1 - 58
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 118 )	A	59 - 118
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 160 )	A	119 - 160
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 92 )	B	2 - 92
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 93 through 109 )	B	93 - 109
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 110 through 159 )	B	110 - 159

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Non-polymers , 5 types, 398 molecules

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 398 molecules

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