PDB-2iir: Acetate kinase from a hypothermophile Thermotoga maritima

ID or keywords:

Entry

Database: PDB / ID: 2iir

Title

Acetate kinase from a hypothermophile Thermotoga maritima

Components

Acetate kinase

Keywords

TRANSFERASE / acetate kinase / thermotoga maritima

Function / homology

Function and homology information

acetate kinase / acetate kinase activity / acetate metabolic process / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Mukhopadhyay, S. / Hasson, M.S. / Sanders, D.A.

Citation

Journal: To be Published
Title: Acetate kinase from a hypothermophile Thermotoga maritima
Authors: Mukhopadhyay, S. / Hasson, M.S. / Sanders, D.A.

History

Deposition	Sep 28, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2iir.cif.gz	707 KB	Display	PDBx/mmCIF format
PDB format	pdb2iir.ent.gz	591.4 KB	Display	PDB format
PDBx/mmJSON format	2iir.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2iir_validation.pdf.gz	504.3 KB	Display	wwPDB validaton report
Full document	2iir_full_validation.pdf.gz	573 KB	Display
Data in XML	2iir_validation.xml.gz	128.4 KB	Display
Data in CIF	2iir_validation.cif.gz	171.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ii/2iir ftp://data.pdbj.org/pub/pdb/validation_reports/ii/2iir	HTTPS FTP

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Related structure data

Related structure data	1g99 1tuu 1tuy
Similar structure data	1tuy-d 4h0o-d 3slc-1 1tuu-d 4fwo-1 3khy-d 3slc-2 4fwl-1 6qdj-d 2o4c-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) 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

1g99

1tuu

1tuy

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Acetate kinase

B: Acetate kinase

C: Acetate kinase

D: Acetate kinase

E: Acetate kinase

F: Acetate kinase

G: Acetate kinase

H: Acetate kinase

I: Acetate kinase

J: Acetate kinase

449 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acetate kinase

B: Acetate kinase

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

2

C: Acetate kinase

D: Acetate kinase

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

3

E: Acetate kinase

F: Acetate kinase

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

4

G: Acetate kinase

H: Acetate kinase

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

5

I: Acetate kinase

J: Acetate kinase

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

Unit cell

Length a, b, c (Å)	105.434, 300.333, 334.898
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-ID	Component-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	MET	MET	GLY	GLY	A	A	1 - 180	1 - 180
2	1	MET	MET	GLY	GLY	B	B	1 - 180	1 - 180
3	1	MET	MET	GLY	GLY	C	C	1 - 180	1 - 180
4	1	MET	MET	GLY	GLY	D	D	1 - 180	1 - 180
5	1	MET	MET	GLY	GLY	E	E	1 - 180	1 - 180
6	1	MET	MET	GLY	GLY	F	F	1 - 180	1 - 180
7	1	MET	MET	GLY	GLY	G	G	1 - 180	1 - 180
8	1	MET	MET	GLY	GLY	H	H	1 - 180	1 - 180
9	1	MET	MET	GLY	GLY	I	I	1 - 180	1 - 180
10	1	MET	MET	GLY	GLY	J	J	1 - 180	1 - 180
11	2	THR	THR	LEU	LEU	A	A	181 - 380	181 - 380
12	2	THR	THR	LEU	LEU	B	B	181 - 380	181 - 380
13	2	THR	THR	LEU	LEU	C	C	181 - 380	181 - 380
14	2	THR	THR	LEU	LEU	D	D	181 - 380	181 - 380
15	2	THR	THR	LEU	LEU	E	E	181 - 380	181 - 380
16	2	THR	THR	LEU	LEU	F	F	181 - 380	181 - 380
17	2	THR	THR	LEU	LEU	G	G	181 - 380	181 - 380
18	2	THR	THR	LEU	LEU	H	H	181 - 380	181 - 380
19	2	THR	THR	LEU	LEU	I	I	181 - 380	181 - 380
20	2	THR	THR	LEU	LEU	J	J	181 - 380	181 - 380
21	3	VAL	VAL	LYS	LYS	A	A	381 - 400	381 - 400
22	3	VAL	VAL	LYS	LYS	B	B	381 - 400	381 - 400
23	3	VAL	VAL	LYS	LYS	C	C	381 - 400	381 - 400
24	3	VAL	VAL	LYS	LYS	D	D	381 - 400	381 - 400
25	3	VAL	VAL	LYS	LYS	E	E	381 - 400	381 - 400
26	3	VAL	VAL	LYS	LYS	F	F	381 - 400	381 - 400
27	3	VAL	VAL	LYS	LYS	G	G	381 - 400	381 - 400
28	3	VAL	VAL	LYS	LYS	H	H	381 - 400	381 - 400
29	3	VAL	VAL	LYS	LYS	I	I	381 - 400	381 - 400
30	3	VAL	VAL	LYS	LYS	J	J	381 - 400	381 - 400

#1: Protein	Acetate kinase Mass: 44867.824 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: ack / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9WYB1, acetate kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.95 Å³/Da / Density % sol: 58.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 100mM Ches, 36% MPD, 50mM Calcium Chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2004
Radiation	Monochromator: APS BEAMLINE 14C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 3.3→99 Å / Num. all: 80503 / Num. obs: 78832 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / B_iso Wilson estimate: 63.144 Å² / R_merge(I) obs: 0.09 / Χ²: 1.066 / Net I/σ(I): 10.5
Reflection shell	Resolution: 3.3→3.42 Å / R_merge(I) obs: 0.264 / Num. unique all: 7039 / Χ²: 1.244 / % possible all: 88.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.3→30 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.92 / SU B: 58.75 / SU ML: 0.432 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	3982	5.1 %	RANDOM
R_work	0.229	-	-	-
obs	0.23	78741	98.2 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 71.231 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.13 Å²	0 Å²	0 Å²
2-	-	-2.07 Å²	0 Å²
3-	-	-	-3.07 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31230	0	0	50	31280

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	31750
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	1.988	42780
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.86	5	3990
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.813	24.545	1320
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.626	15	6020
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.773	15	170
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	4840
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	23290
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	14017
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	21382
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	869
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.396	0.2	134
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.469	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	0.147	1.5	20301
X-RAY DIFFRACTION	r_mcangle_it	0.229	2	31970
X-RAY DIFFRACTION	r_scbond_it	0.349	3	12661
X-RAY DIFFRACTION	r_scangle_it	0.538	4.5	10810

Refine LS restraints NCS

Ens-ID: 1 / Number: 3122 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	TIGHT POSITIONAL	0.03	0.05
2	B	TIGHT POSITIONAL	0.03	0.05
3	C	TIGHT POSITIONAL	0.04	0.05
4	D	TIGHT POSITIONAL	0.05	0.05
5	E	TIGHT POSITIONAL	0.05	0.05
6	F	TIGHT POSITIONAL	0.04	0.05
7	G	TIGHT POSITIONAL	0.05	0.05
8	H	TIGHT POSITIONAL	0.03	0.05
9	I	TIGHT POSITIONAL	0.03	0.05
10	J	TIGHT POSITIONAL	0.05	0.05
1	A	TIGHT THERMAL	0.05	0.5
2	B	TIGHT THERMAL	0.04	0.5
3	C	TIGHT THERMAL	0.05	0.5
4	D	TIGHT THERMAL	0.05	0.5
5	E	TIGHT THERMAL	0.05	0.5
6	F	TIGHT THERMAL	0.05	0.5
7	G	TIGHT THERMAL	0.05	0.5
8	H	TIGHT THERMAL	0.05	0.5
9	I	TIGHT THERMAL	0.05	0.5
10	J	TIGHT THERMAL	0.05	0.5

LS refinement shell

Resolution: 3.3→3.383 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.334	249	-
R_work	0.321	4894	-
obs	-	5143	89.24 %

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	2.6583	-2.0097	0.2687	5.8978	-0.4792	1.683	0.4111	-0.0823	0.6893	0.6823	-0.3328	-0.0905	-0.4584	-0.1544	-0.0783	-0.0668	-0.3739	0.3518	-0.1682	-0.0995	-0.2231	23.4343	106.1823	62.6394
2	2.7986	-0.0411	0.4724	3.1077	0.8886	3.1386	0.3618	-0.3684	0.2222	1.0407	-0.3625	0.5244	-0.2228	-0.4572	0.0007	0.0683	-0.3766	0.3149	-0.0578	-0.0715	-0.3714	17.342	84.8676	73.6215
3	3.6369	-2.5956	-0.2578	6.0222	0.2892	1.703	0.3462	-0.0854	-0.7942	0.6846	-0.2949	0.1778	0.4504	0.1748	-0.0513	-0.0261	-0.3668	-0.3064	-0.2076	0.0461	-0.2047	29.3702	46.6873	62.6
4	2.5588	-0.1877	-0.0972	3.0593	-0.8048	3.4883	0.3852	-0.3747	-0.1783	1.0257	-0.3584	-0.4458	0.3205	0.529	-0.0267	0.0652	-0.3721	-0.2744	-0.0516	0.0364	-0.3877	35.4184	67.9941	73.6113
5	1.8593	0.1927	-0.2043	4.4411	3.2372	6.1109	0.0311	0.4653	-0.4119	0.1576	0.045	-0.355	0.6328	-0.3731	-0.0761	-0.4053	-0.1849	0.1997	-0.3088	-0.0675	-0.2098	59.4195	103.4021	37.6229
6	2.8589	-0.7605	-0.3102	3.8295	0.3813	2.6428	-0.101	0.6365	-0.6071	-0.1495	-0.0198	-0.6199	-0.0421	0.2474	0.1208	-0.4389	-0.1218	0.1954	-0.2786	-0.1488	-0.2966	76.6255	120.4733	42.3945
7	1.8954	-0.7728	-0.5076	5.2456	2.6154	2.9445	-0.1874	-0.1048	0.2484	0.2945	0.1629	-0.5738	-0.4213	0.0401	0.0246	-0.1671	-0.108	-0.1222	-0.4201	0.0827	-0.4229	70.8334	156.9882	61.0296
8	4.6588	0.1093	0.5947	2.7283	0.2701	2.6676	-0.3536	-0.3152	-0.0885	0.7046	0.1828	-0.4961	-0.1467	-0.02	0.1708	-0.1641	-0.0249	-0.025	-0.422	-0.0029	-0.5263	73.5587	132.5185	63.665
9	1.692	-0.659	0.3702	5.5288	-2.4528	2.5588	-0.2022	-0.0842	-0.2431	0.2122	0.1944	0.543	0.4016	-0.0391	0.0078	-0.2028	-0.1147	0.1319	-0.386	-0.096	-0.4149	87.3831	-4.1166	60.9578
10	4.5711	0.0468	-0.8598	2.7015	-0.1296	2.6478	-0.3343	-0.3637	0.0938	0.606	0.18	0.5079	0.1702	0.0421	0.1543	-0.2031	-0.0317	0.0182	-0.4116	-0.0119	-0.5118	84.6589	20.353	63.5824
11	1.9846	0.4968	0.0659	3.5471	-2.7	6.2846	-0.0258	0.4693	0.4181	0.1572	-0.0152	0.3483	-0.6888	0.4319	0.041	-0.3621	-0.1976	-0.1987	-0.3372	0.0396	-0.2157	98.9062	49.4184	37.5224
12	3.235	-1.0361	-0.128	4.612	-0.0876	2.1051	-0.0446	0.5631	0.5771	-0.2684	-0.0139	0.6415	-0.0219	-0.1865	0.0585	-0.4856	-0.1137	-0.2024	-0.2525	0.1325	-0.3104	81.6806	32.3677	42.2804
13	4.8863	1.5455	1.3638	3.0963	0.5123	2.896	0.1228	-0.1215	-0.6045	-0.2227	0.1219	-0.0647	0.3854	-0.4998	-0.2447	-0.0406	-0.1453	-0.162	-0.3629	0.1028	-0.5453	8.8386	19.8363	20.2093
14	2.9022	0.3263	0.4817	3.4918	0.9449	3.5898	-0.0456	0.2643	0.0866	-0.6542	0.0705	-0.0965	0.1922	-0.4082	-0.0249	-0.3277	-0.0837	-0.085	-0.2842	0.0555	-0.4955	23.174	37.8559	11.2943
15	4.6543	1.9119	1.9023	3.4697	1.6465	2.8852	0.0146	-0.2924	0.093	-0.0928	0.0219	-0.5758	-0.1312	0.1511	-0.0365	-0.5113	0.0111	-0.0252	-0.4546	0.037	-0.1099	45.19	64.7978	33.5866
16	3.6877	1.0056	-0.8632	3.1412	-0.5987	2.9462	0.0348	-0.1048	-0.1043	-0.0701	0.1297	-0.9404	0.1788	0.329	-0.1644	-0.5113	0.0596	-0.1508	-0.3807	-0.1135	-0.1239	43.6021	41.94	24.2618
17	4.4465	1.7773	-1.7643	3.3113	-1.2687	2.7669	0.0261	-0.2827	-0.0729	-0.156	0.0249	0.5999	0.2073	-0.1179	-0.051	-0.457	-0.0033	0.003	-0.442	-0.1	-0.0505	7.5437	88.1241	33.6178
18	3.5453	0.8969	0.976	3.0736	0.3367	3.4192	0.0204	-0.0534	0.0949	-0.125	0.0911	0.9967	-0.1854	-0.3287	-0.1116	-0.4527	0.0292	0.0904	-0.3839	0.0053	-0.0639	9.2637	110.9753	24.2872
19	5.8104	1.6982	-2.24	3.1403	-0.2248	3.194	0.0917	-0.0807	0.5318	-0.2658	0.1779	0.0752	-0.518	0.4679	-0.2695	-0.1061	-0.142	0.1191	-0.3922	-0.1046	-0.5256	44.1919	132.8884	20.1592
20	2.7323	0.4873	-0.3376	3.1922	-0.8181	3.9724	-0.0497	0.327	-0.0369	-0.7661	0.0812	0.1215	-0.0792	0.5045	-0.0315	-0.2672	-0.1023	0.097	-0.2333	-0.123	-0.4592	29.7624	114.9092	11.289

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 179	1 - 179
2	1	A	A	383 - 400	383 - 400
3	2	A	A	180 - 382	180 - 382
4	3	B	B	1 - 179	1 - 179
5	3	B	B	383 - 400	383 - 400
6	4	B	B	180 - 382	180 - 382
7	5	C	C	1 - 179	1 - 179
8	5	C	C	383 - 400	383 - 400
9	6	C	C	180 - 382	180 - 382
10	7	D	D	1 - 179	1 - 179
11	7	D	D	383 - 400	383 - 400
12	8	D	D	180 - 382	180 - 382
13	9	E	E	1 - 179	1 - 179
14	9	E	E	383 - 400	383 - 400
15	10	E	E	180 - 382	180 - 382
16	11	F	F	1 - 179	1 - 179
17	11	F	F	383 - 400	383 - 400
18	12	F	F	180 - 382	180 - 382
19	13	G	G	1 - 179	1 - 179
20	13	G	G	383 - 400	383 - 400
21	14	G	G	180 - 382	180 - 382
22	15	H	H	1 - 179	1 - 179
23	15	H	H	383 - 400	383 - 400
24	16	H	H	180 - 382	180 - 382
25	17	I	I	1 - 179	1 - 179
26	17	I	I	383 - 400	383 - 400
27	18	I	I	180 - 382	180 - 382
28	19	J	J	1 - 179	1 - 179
29	19	J	J	383 - 400	383 - 400
30	20	J	J	180 - 382	180 - 382

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