PDB-5xu7: Crystal structure of Escherichia coli holo-[acyl-carrier-protein]...

ID or keywords:

Entry

Database: PDB / ID: 5xu7

Title

Crystal structure of Escherichia coli holo-[acyl-carrier-protein] synthase (AcpS)

Components

Holo-[acyl-carrier-protein] synthase

Keywords

TRANSFERASE / Gram-negative bacteria / phosphopantetheinyl transferase / homotrimer

Function / homology

Function and homology information

holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / transferase activity / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 Å

Authors

Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S.

Citation

Journal: To Be Published
Title: Crystal structures of acyl carrier protein synthases (AcpS) from three Gram-negative bacteria
Authors: Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S.

History

Deposition	Jun 22, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 27, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5xu7.cif.gz	173.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5xu7.ent.gz	138.8 KB	Display	PDB format
PDBx/mmJSON format	5xu7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5xu7_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	5xu7_full_validation.pdf.gz	450 KB	Display
Data in XML	5xu7_validation.xml.gz	18.9 KB	Display
Data in CIF	5xu7_validation.cif.gz	27.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xu/5xu7 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/5xu7	HTTPS FTP

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Related structure data

Related structure data	5xuhC 5xukC 5xumC 3qmnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cmo-d 5xuh-d 3ne3-2 6c3z-d 5vbx-d 1aop-d 3eby-1 6ljo-1 6lis-2 3wg9-2 Search similar-shape structures by Omokage search (details) 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: Holo-[acyl-carrier-protein] synthase

B: Holo-[acyl-carrier-protein] synthase

C: Holo-[acyl-carrier-protein] synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	97.620, 97.620, 96.140
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-373- HOH
2	1	B-268- HOH

#1: Protein	Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase AcpS Mass: 14074.297 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acpS, dpj, b2563, JW2547 / Production host: Escherichia coli (E. coli) References: UniProt: P24224, holo-[acyl-carrier-protein] synthase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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.: 358 / 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: 2.71 Å³/Da / Density % sol: 54.65 %
Crystal grow	Temperature: 277 K / Method: evaporation / pH: 8 Details: 10mM Tris-HCl pH 8.0, 100mM NaCl, 10mM MgCl2, 1mM DTT

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2013
Radiation	Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.84→48.81 Å / Num. obs: 40765 / % possible obs: 99.4 % / Redundancy: 12.7 % / B_iso Wilson estimate: 24.3 Å² / R_merge(I) obs: 0.083 / R_pim(I) all: 0.024 / Net I/σ(I): 19
Reflection shell	Resolution: 1.84→1.94 Å / Redundancy: 12.6 % / R_merge(I) obs: 0.603 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5866 / R_pim(I) all: 0.176 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QMN

3qmn

Resolution: 1.84→30 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.943 / SU B: 5.475 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21357	2042	5 %	RANDOM
R_work	0.17528	-	-	-
obs	0.17719	38660	99.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 34.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.69 Å²	0 Å²	0 Å²
2-	-	0.69 Å²	0 Å²
3-	-	-	-1.37 Å²

Refinement step

Cycle: 1 / Resolution: 1.84→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2833	0	9	358	3200

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	2925
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.99	1.941	3952
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.107	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.462	22.263	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.135	15	511
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.349	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	446
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2196
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	1.2	3	2924
X-RAY DIFFRACTION	r_sphericity_free	23.362	5	114
X-RAY DIFFRACTION	r_sphericity_bonded	5.103	5	3117

LS refinement shell

Resolution: 1.839→1.887 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.25	118	-
R_work	0.215	2600	-
obs	-	-	99.71 %

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	1.5513	-1.4127	0.6389	3.2313	-2.2697	3.2371	-0.0717	0.0111	0.1085	-0.1089	-0.0525	-0.2274	-0.0088	-0.0577	0.1243	0.0903	0.001	0.0006	0.0918	0.0012	0.1221	36.4877	-14.9429	-11.3529
2	2.817	-0.0475	0.5217	2.9522	0.3042	1.7354	-0.0927	0.2894	-0.1061	-0.2611	-0.0093	-0.075	0.0013	-0.0235	0.102	0.1323	-0.0285	-0.004	0.1252	-0.0273	0.078	33.7348	-21.0667	-23.674
3	3.7993	-2.312	2.59	2.4549	-1.9753	3.915	-0.085	0.0687	-0.1292	-0.1201	0.0219	0.0126	0.1248	0.0664	0.0632	0.1066	-0.0126	0.0167	0.0982	-0.0196	0.1166	35.7779	-20.923	-12.4655
4	2.7317	-0.29	1.1965	3.3681	-1.1606	3.8302	-0.293	0.1092	-0.0155	-0.1231	-0.024	-0.3586	0.1185	0.2191	0.317	0.1203	0.0387	0.0218	0.104	-0.0287	0.145	40.838	-27.161	-14.5206
5	50.4303	26.2814	-20.1636	35.0027	-38.3565	44.4692	-0.98	-0.4369	-0.68	-1.4859	1.5283	0.4901	1.6096	-1.8143	-0.5483	0.3602	-0.2589	0.0976	0.406	0.1095	0.656	25.8632	-36.3663	-10.3787
6	9.8762	-1.6389	1.6615	3.4273	-0.0924	3.5842	-0.2508	0.304	-0.5944	-0.1704	-0.037	-0.1431	0.3046	0.1952	0.2877	0.1432	0.0153	0.0771	0.0331	0.0043	0.1756	44.43	-33.8781	-12.4732
7	3.0633	-2.6354	-0.1469	4.5866	-0.4552	0.9167	-0.1728	-0.0641	-0.2837	0.0873	0.073	0.1593	0.0994	-0.0048	0.0998	0.1016	0.0099	0.0268	0.1012	0.0081	0.1396	34.0227	-24.9576	-4.685
8	1.1774	-0.2419	-0.7566	2.6282	-0.4952	1.2102	0.0261	0.0331	0.0489	-0.1209	0.0289	0.2641	0.1199	-0.2313	-0.055	0.0943	-0.0273	-0.0061	0.1516	-0.0111	0.153	17.133	-17.8949	1.9569
9	1.6351	-0.3527	-0.5087	3.9797	-0.2297	1.0147	0.0249	-0.1813	-0.0385	0.3497	-0.1078	0.2244	0.0125	-0.068	0.0828	0.1021	-0.0426	0.0595	0.1433	-0.0148	0.1224	17.3794	-17.9783	10.2444
10	3.6906	-0.1942	-2.777	2.1998	-0.4128	2.2337	-0.0523	-0.3416	-0.3578	0.1101	-0.1505	0.2484	0.0169	0.2849	0.2027	0.18	-0.0714	0.0801	0.1773	0.0576	0.1239	22.4886	-26.8712	12.3281
11	1.9552	0.475	-0.6109	1.4871	-0.3714	0.9443	-0.0969	-0.3053	-0.267	0.0907	-0.0898	-0.0087	0.1673	0.0423	0.1867	0.1411	0.016	0.0651	0.1419	0.048	0.1241	26.0292	-27.7182	8.534
12	0.1578	0.0898	-0.1075	2.5202	0.0927	0.4728	-0.0583	-0.2091	0.0049	0.1202	0.1456	0.0056	-0.0044	0.1653	-0.0873	0.1483	0.0536	0.0146	0.321	-0.0264	0.1369	39.6152	-5.6294	9.1634
13	5.4356	-0.9485	4.0259	12.9584	-2.0296	9.7913	-0.1049	-0.2474	0.0598	-0.0431	0.0621	-1.1339	-0.5042	1.0997	0.0428	0.0316	-0.0675	0.0163	0.4615	-0.0615	0.1762	52.6033	-3.4031	6.2877
14	2.2362	2.2343	-1.5857	9.2524	-4.7429	4.9622	0.1318	-0.485	0.0458	0.2078	-0.0986	-0.1501	0.0256	0.6375	-0.0332	0.088	0.0251	-0.0195	0.2437	-0.0494	0.0554	42.3349	-10.6981	7.4535
15	0.2904	-2.6153	0.6827	25.1791	-6.4559	1.6632	0.0533	0.0608	0.0008	1.7694	-0.232	0.0194	-0.4176	0.1225	0.1787	0.3052	0.0494	-0.0261	0.8937	-0.0503	0.0891	47.621	-13.8411	13.0059
16	45.1852	-36.7664	6.6975	47.3615	28.3695	66.556	2.4502	2.9952	-1.2311	-0.8871	-1.9401	0.8359	2.4461	1.3585	-0.5101	0.5503	0.3262	0.1312	0.8311	0.143	0.4473	55.3543	-20.4478	-1.0501
17	9.0456	2.2834	-4.9443	3.0793	4.0518	14.7697	-0.0369	-0.3419	-0.2125	0.0929	0.1448	-0.2402	0.2724	1.0019	-0.1079	0.1042	0.1861	-0.0768	0.5796	0.0469	0.2029	51.8261	-17.9559	10.6683
18	1.1217	-0.0508	-0.1603	1.6135	-0.1095	1.7841	-0.0285	-0.3927	-0.0491	0.1991	0.0864	-0.0362	0.1252	0.3821	-0.0579	0.1201	0.0657	-0.0151	0.2715	0.02	0.0882	43.1603	-19.8158	8.9816

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 23
2	X-RAY DIFFRACTION	2	A	24 - 45
3	X-RAY DIFFRACTION	3	A	46 - 64
4	X-RAY DIFFRACTION	4	A	65 - 81
5	X-RAY DIFFRACTION	5	A	82 - 86
6	X-RAY DIFFRACTION	6	A	87 - 102
7	X-RAY DIFFRACTION	7	A	103 - 126
8	X-RAY DIFFRACTION	8	B	2 - 31
9	X-RAY DIFFRACTION	9	B	32 - 63
10	X-RAY DIFFRACTION	10	B	64 - 86
11	X-RAY DIFFRACTION	11	B	87 - 126
12	X-RAY DIFFRACTION	12	C	2 - 31
13	X-RAY DIFFRACTION	13	C	32 - 45
14	X-RAY DIFFRACTION	14	C	46 - 64
15	X-RAY DIFFRACTION	15	C	65 - 81
16	X-RAY DIFFRACTION	16	C	82 - 86
17	X-RAY DIFFRACTION	17	C	87 - 92
18	X-RAY DIFFRACTION	18	C	93 - 126

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