PDB-1qzt: Phosphotransacetylase from Methanosarcina thermophila

ID or keywords:

Entry

Database: PDB / ID: 1qzt

Title

Phosphotransacetylase from Methanosarcina thermophila

Components

Phosphate acetyltransferase

Keywords

TRANSFERASE / Phosphotransacetylase (Pta) / Coenzyme A (CoA) / Acetyl Coenzyme A (Acetyl CoA) / Acetyl phosphate / Acetate Metabolism

Function / homology

Function and homology information

phosphate acetyltransferase activity / phosphate acetyltransferase / acetyl-CoA biosynthetic process / plasma membrane
Similarity search - Function

Biological species

Methanosarcina thermophila (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.7 Å

Authors

Iyer, P.P. / Lawrence, S.H. / Luther, K.B. / Rajashankar, K.R. / Yennawar, H.P. / Ferry, J.G. / Schindelin, H.

Citation

Journal: STRUCTURE / Year: 2004
Title: Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila.
Authors: Iyer, P.P. / Lawrence, S.H. / Luther, K.B. / Rajashankar, K.R. / Yennawar, H.P. / Ferry, J.G. / Schindelin, H.

History

Deposition	Sep 17, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 22, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jun 27, 2018	Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4	Jan 15, 2020	Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5	Feb 14, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site 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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1qzt.cif.gz	479.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1qzt.ent.gz	402.2 KB	Display	PDB format
PDBx/mmJSON format	1qzt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1qzt_validation.pdf.gz	467.1 KB	Display	wwPDB validaton report
Full document	1qzt_full_validation.pdf.gz	494.3 KB	Display
Data in XML	1qzt_validation.xml.gz	48 KB	Display
Data in CIF	1qzt_validation.cif.gz	66.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qz/1qzt ftp://data.pdbj.org/pub/pdb/validation_reports/qz/1qzt	HTTPS FTP

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Related structure data

Related structure data	1qzs PDB Unreleased entry
Similar structure data	2af3-d 6iox-d 2qzx-d 1xco-4 5eii-1 1xco-3 1r5j-d 1xco-2 3isx-1 4ig4-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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1qzs
PDB Unreleased entry

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphate acetyltransferase

B: Phosphate acetyltransferase

C: Phosphate acetyltransferase

D: Phosphate acetyltransferase

hetero molecules

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

1

A: Phosphate acetyltransferase

B: Phosphate acetyltransferase

hetero molecules

defined by author&software
71.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phosphate acetyltransferase

D: Phosphate acetyltransferase

hetero molecules

defined by author&software
70.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: Phosphate acetyltransferase

B: Phosphate acetyltransferase

hetero molecules

C: Phosphate acetyltransferase

D: Phosphate acetyltransferase

hetero molecules

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

4

B: Phosphate acetyltransferase

hetero molecules

A: Phosphate acetyltransferase

hetero molecules

C: Phosphate acetyltransferase

D: Phosphate acetyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.345, 115.345, 129.366
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Cell setting	tetragonal
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
1	2
2	2
3	2
4	2
1	3
2	3
3	3
1	4
2	4
3	4

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	ILE	ILE	A	A	11 - 138	11 - 138
2	1	ARG	ARG	ILE	ILE	B	B	11 - 138	11 - 138
3	1	ARG	ARG	ILE	ILE	C	C	11 - 138	11 - 138
4	1	ARG	ARG	ILE	ILE	D	D	11 - 138	11 - 138
1	2	PHE	PHE	GLY	GLY	A	A	151 - 295	151 - 295
2	2	PHE	PHE	GLY	GLY	B	B	151 - 295	151 - 295
3	2	PHE	PHE	GLY	GLY	C	C	151 - 295	151 - 295
4	2	PHE	PHE	GLY	GLY	D	D	151 - 295	151 - 295
1	3	PRO	PRO	GLN	GLN	A	A	296 - 331	296 - 331
2	3	PRO	PRO	GLN	GLN	B	B	296 - 331	296 - 331
3	3	PRO	PRO	GLN	GLN	C	C	296 - 331	296 - 331
1	4	THR	THR	GLU	GLU	A	A	3 - 10	3 - 10
2	4	THR	THR	GLU	GLU	C	C	3 - 10	3 - 10
3	4	THR	THR	GLU	GLU	D	D	3 - 10	3 - 10

NCS ensembles :

ID
1
2
3
4

#1: Protein	Phosphate acetyltransferase / Phosphotransacetylase Mass: 35257.492 Da / Num. of mol.: 4 / Fragment: Phosphotransacetylase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina thermophila (archaea) / Gene: PTA / Plasmid: pML702 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P38503, phosphate acetyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.05 Å³/Da / Density % sol: 59.67 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium acetate, ammonium sulfate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. all: 49910 / Num. obs: 49910 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_merge(I) obs: 0.084 / R_sym value: 0.084
Reflection shell	Resolution: 2.6→2.69 Å / % possible all: 97.9

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing

Refinement

Resolution: 2.7→20 Å / Cor.coef. F_o:F_c: 0.916 / Cor.coef. F_o:F_c free: 0.889 / SU B: 13.605 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 1.323 / ESU R Free: 0.385 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28636	2225	5 %	RANDOM
R_work	0.24667	-	-	-
obs	0.24864	42640	96.75 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 43.046 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.07 Å²	0 Å²	0 Å²
2-	-	2.07 Å²	0 Å²
3-	-	-	-4.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9832	0	55	102	9989

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	10010
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9392
X-RAY DIFFRACTION	r_angle_refined_deg	1.549	1.984	13564
X-RAY DIFFRACTION	r_angle_other_deg	0.902	3	21950
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.859	5	1322
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1630
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11070
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1742
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	2475
X-RAY DIFFRACTION	r_nbd_other	0.245	0.2	10977
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	5847
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	179
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.266	0.2	35
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.263	0.2	115
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.278	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.862	1.5	6602
X-RAY DIFFRACTION	r_mcangle_it	1.64	2	10588
X-RAY DIFFRACTION	r_scbond_it	1.97	3	3408
X-RAY DIFFRACTION	r_scangle_it	3.392	4.5	2976

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	758	tight positional	0.09	0.1
1	2	B	758	tight positional	0.09	0.1
1	3	C	758	tight positional	0.09	0.1
1	4	D	758	tight positional	0.07	0.1
2	1	A	853	tight positional	0.09	0.1
2	2	B	853	tight positional	0.1	0.1
2	3	C	853	tight positional	0.08	0.1
2	4	D	853	tight positional	0.09	0.1
3	1	A	211	tight positional	0.16	0.1
3	2	B	211	tight positional	0.23	0.1
3	3	C	211	tight positional	0.12	0.1
4	1	A	48	tight positional	0.07	0.1
4	2	C	48	tight positional	0.08	0.1
4	3	D	48	tight positional	0.07	0.1
1	1	A	1170	medium positional	0.15	0.2
1	2	B	1170	medium positional	0.16	0.2
1	3	C	1170	medium positional	0.16	0.2
1	4	D	1170	medium positional	0.13	0.2
2	1	A	1217	medium positional	0.16	0.2
2	2	B	1217	medium positional	0.17	0.2
2	3	C	1217	medium positional	0.15	0.2
2	4	D	1217	medium positional	0.25	0.2
3	1	A	277	medium positional	0.23	0.2
3	2	B	277	medium positional	0.31	0.2
3	3	C	277	medium positional	0.16	0.2
4	1	A	82	medium positional	0.12	0.2
4	2	C	82	medium positional	0.12	0.2
4	3	D	82	medium positional	0.16	0.2
1	1	A	758	tight thermal	8.54	8
1	2	B	758	tight thermal	2.57	8
1	3	C	758	tight thermal	12.84	8
1	4	D	758	tight thermal	18.17	8
2	1	A	853	tight thermal	2.31	8
2	2	B	853	tight thermal	2.23	8
2	3	C	853	tight thermal	2.05	8
2	4	D	853	tight thermal	2.29	8
3	1	A	211	tight thermal	4.52	8
3	2	B	211	tight thermal	4.66	8
3	3	C	211	tight thermal	4.96	8
4	1	A	48	tight thermal	4.07	8
4	2	C	48	tight thermal	1.74	8
4	3	D	48	tight thermal	5.74	8
1	1	A	1170	medium thermal	8.74	8
1	2	B	1170	medium thermal	3.38	8
1	3	C	1170	medium thermal	12.26	8
1	4	D	1170	medium thermal	17.61	8
2	1	A	1217	medium thermal	2.75	8
2	2	B	1217	medium thermal	3.09	8
2	3	C	1217	medium thermal	2.63	8
2	4	D	1217	medium thermal	2.8	8
3	1	A	277	medium thermal	5.19	8
3	2	B	277	medium thermal	5.5	8
3	3	C	277	medium thermal	5.05	8
4	1	A	82	medium thermal	3.92	8
4	2	C	82	medium thermal	2.35	8
4	3	D	82	medium thermal	5.76	8

LS refinement shell

Resolution: 2.7→2.769 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.379	159
R_work	0.32	3138

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	0.5243	0.2696	0.0585	0.5945	-0.3081	0.4489	0.0507	-0.0352	0.0503	0.1031	0.007	0.0059	-0.0656	-0.0363	-0.0578	0.1013	0.0026	0.02	0.0674	0.0152	0.0649	3.6972	62.4035	14.7174
2	6.04	-1.1645	-1.622	0.0433	2.6215	-1.227	-0.1026	0.271	-0.3963	0.2098	-0.0765	0.3101	0.2191	0.0926	0.1792	0.2015	-0.0218	0.0102	0.02	0.0321	0.1425	7.716	54.0547	-3.084
3	0.3053	-0.0029	0.0565	0.5473	0.0217	0.3286	0.0511	0.0597	0.0333	0.0157	-0.0311	-0.0163	0.0003	-0.0005	-0.02	0.0771	-0.0037	0.0039	0.0793	0.0391	0.1043	26.3617	55.7512	-7.386
4	0.7984	0.2663	0.6451	0.0201	0.1983	1.5757	0.1028	-0.0724	0.0189	0.1004	-0.0092	0.0284	-0.0815	-0.006	-0.0937	0.1086	-0.0224	-0.0061	0.0639	0.0054	0.1057	12.9585	63.3813	8.2468
5	0.5975	0.2533	-0.0431	0.8983	0.2655	1.1471	0.0443	0.0638	0.0259	-0.0773	-0.0355	-0.1637	-0.0041	0.1334	-0.0089	0.0385	0.0343	0.0486	0.0474	0.0444	0.1408	58.8405	40.4447	-17.4292
6	5.917	0.8357	-4.3816	1.6381	5.0409	0.6415	0.2923	-0.0589	-0.4196	0.1507	-0.6063	-0.181	-0.0438	-0.0236	0.314	0.08	0.0356	-0.0248	0.0567	0.0618	0.1376	47.4755	28.5655	-6.2784
7	0.4774	-0.024	-0.0333	0.5601	0.0137	0.2484	0.0201	0.0101	0.0091	0.066	-0.0355	-0.0367	0.023	0.0125	0.0154	0.0887	-0.008	-0.0256	0.0688	0.01	0.1037	38.0227	42.5091	5.9102
8	-0.3736	-0.3676	-0.6405	0.3073	0.0085	1.4529	0.0335	0.0667	0.1117	-0.1726	-0.0458	-0.1524	0.1434	0.0797	0.0123	0.0547	0.0253	-0.0124	0.0768	0.0547	0.1408	53.5272	42.3142	-7.3225
9	0.4243	0.1653	-0.1142	0.6564	-0.2567	0.3988	0.0105	0.028	0.0421	-0.0027	0.0371	0.0246	-0.0344	-0.0197	-0.0476	0.0685	0.0007	0.0176	0.0638	0.0191	0.086	57.1654	120.8728	80.7277
10	2.7977	1.5051	-1.6062	0.3582	-1.2546	3.6353	0.2332	0.1712	0.1075	-0.3669	-0.0141	0.029	-0.0781	-0.2691	-0.2191	0.1732	0.0129	0.0176	0.0701	0.0107	0.0658	64.0468	115.2053	63.7518
11	0.4469	-0.1109	0.0379	0.4887	-0.0454	0.3873	0.0271	0.0613	0.0306	0.0154	-0.0452	-0.0191	-0.017	0.0243	0.0181	0.0752	-0.0013	0.0129	0.0916	0.0554	0.0982	83.1264	116.7699	61.939
12	0.7966	-0.1086	-0.3149	-0.4377	-0.5093	1.2232	-0.0124	0.0415	0.079	0.0188	-0.0585	-0.0363	-0.0298	0.0036	0.0709	0.0898	-0.0152	0.0346	0.0635	0.0295	0.11	67.6735	122.6206	76.2822
13	0.875	0.0298	0.1383	0.4521	0.4676	2.1718	0.0677	0.1556	-0.0437	-0.3247	0.0534	-0.2184	-0.0796	0.3377	-0.1211	0.1683	0.0369	0.0207	0.1533	0.0239	0.1645	117.1228	97.0563	55.1029
14	1.4145	5.9464	-2.9805	-3.7427	0.2306	1.769	-0.2363	-0.2731	-0.5104	-0.1995	0.0666	0.2436	0.2642	0.1429	0.1697	0.0871	0.0347	0.0158	0.0999	0.07	0.1487	103.122	89.1624	64.8142
15	0.8209	-0.2807	0.1806	0.8759	-0.0708	-0.178	-0.0132	-0.0109	-0.0071	0.0701	-0.0318	-0.0245	0.0157	0.0095	0.045	0.0888	-0.0094	-0.0262	0.0817	0.0492	0.0853	92.8059	102.4334	75.7625
16	0.6833	0.0997	0.8019	2.7517	-0.6241	2.3451	-0.0135	0.132	-0.0598	-0.1638	0.0414	-0.1143	-0.149	0.3003	-0.0279	0.0509	-0.0016	0.0027	0.1419	0.0854	0.0979	110.9962	100.9731	64.1784

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 138	3 - 138
2	X-RAY DIFFRACTION	2	A	A	139 - 150	139 - 150
3	X-RAY DIFFRACTION	3	A	A	151 - 295	151 - 295
4	X-RAY DIFFRACTION	4	A	A	296 - 333	296 - 333
5	X-RAY DIFFRACTION	5	B	B	3 - 138	3 - 138
6	X-RAY DIFFRACTION	6	B	B	139 - 150	139 - 150
7	X-RAY DIFFRACTION	7	B	B	151 - 295	151 - 295
8	X-RAY DIFFRACTION	8	B	B	296 - 332	296 - 332
9	X-RAY DIFFRACTION	9	C	C	3 - 138	3 - 138
10	X-RAY DIFFRACTION	10	C	C	139 - 150	139 - 150
11	X-RAY DIFFRACTION	11	C	C	151 - 295	151 - 295
12	X-RAY DIFFRACTION	12	C	C	296 - 332	296 - 332
13	X-RAY DIFFRACTION	13	D	D	3 - 138	3 - 138
14	X-RAY DIFFRACTION	14	D	D	139 - 150	139 - 150
15	X-RAY DIFFRACTION	15	D	D	151 - 295	151 - 295
16	X-RAY DIFFRACTION	16	D	D	296 - 333	296 - 333

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Yorodumi