PDB-3hpq: Crystal structure of wild-type adenylate kinase from E. coli, in ...

ID or keywords:

Entry

Database: PDB / ID: 3hpq

Title

Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A

Components

Adenylate kinase

Keywords

TRANSFERASE /

Enzyme Inhibitor Complex / ATP-binding /

Kinase / Nucleotide biosynthesis / Nucleotide-binding

Function / homology

Function and homology information

purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process /

adenylate kinase /

adenylate kinase activity / AMP salvage /

nucleoside diphosphate kinase activity / AMP binding /

phosphorylation ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Hilser, V.J. / Travis, T.P. / Bolen, D.W.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins.
Authors: Schrank, T.P. / Bolen, D.W. / Hilser, V.J.

History

Deposition	Jun 4, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Sep 6, 2023	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 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3hpq.cif.gz	197.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3hpq.ent.gz	158.9 KB	Display	PDB format
PDBx/mmJSON format	3hpq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpq ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpq	HTTPS FTP

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Related structure data

Related structure data	3hprC 1akeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1e4v-1 4jzk-1 5eje-1 4x8l-1 3hpr-2 1e4y-1 1e4y-2 1ake-2 4x8o-1 4x8l-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Adenylate kinase

B: Adenylate kinase

hetero molecules

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

1

A: Adenylate kinase

hetero molecules

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

2

B: Adenylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.646, 72.639, 78.699
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-564- HOH
2	1	B-234- HOH
3	1	B-458- HOH
4	1	B-600- HOH

#1: Protein	Adenylate kinase / / AK / ATP-AMP transphosphorylase Mass: 23620.029 Da / Num. of mol.: 2 / Mutation: Wild-type Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: adk, b0474, dnaW, JW0463, plsA / Plasmid: pEAK91 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P69441, adenylate kinase
#2: Chemical	ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₉N₁₀O₂₂P₅
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.53 Å³/Da / Density % sol: 51.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 45 mg/ml AK in 50 mM MES pH 6.7, 1 mM EDTA, with 50% 50mM MES pH 7.0-7.3, 3% w/v PEG 2000 and 1.8-2.3 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K PH range: 7.0-7.3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
Detector	Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 1, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 36651 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / R_merge(I) obs: 0.046 / Net I/σ(I): 47.55
Reflection shell	Resolution: 1.9→2.03 Å / R_merge(I) obs: 0.159 / Mean I/σ(I) obs: 9.06 / Num. unique all: 3048 / % possible all: 82.8

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Processing

Software

Name	Classification
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1AKE

1ake

Resolution: 2→14.999 Å / SU ML: 0.29 / Isotropic thermal model: anisotropic (tls) / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2454	3277	9.94 %	RANDOM
R_work	0.1994	-	-	-
obs	0.204	32979	99.93 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 82.657 Å² / k_sol: 0.381 e/Å³

Displacement parameters

B_iso mean: 34.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4442 Å²	0 Å²	0 Å²
2-	-	0.0313 Å²	0 Å²
3-	-	-	-0.4755 Å²

Refinement step

Cycle: LAST / Resolution: 2→14.999 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3312	0	114	661	4087

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_bond_d	0.011
X-RAY DIFFRACTION	f_angle_d	1.511
X-RAY DIFFRACTION	f_dihedral_angle_d	22.879
X-RAY DIFFRACTION	f_chiral_restr	0.052
X-RAY DIFFRACTION	f_plane_restr	0.004

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 (%)
2-2.0298	0.2891	145	0.242	1270	X-RAY DIFFRACTION	100
2.0298-2.0615	0.2782	141	0.2413	1279	X-RAY DIFFRACTION	100
2.0615-2.0952	0.2927	141	0.2341	1277	X-RAY DIFFRACTION	100
2.0952-2.1312	0.2785	139	0.2321	1280	X-RAY DIFFRACTION	100
2.1312-2.1698	0.3106	128	0.217	1259	X-RAY DIFFRACTION	100
2.1698-2.2114	0.3034	141	0.223	1286	X-RAY DIFFRACTION	100
2.2114-2.2564	0.2905	136	0.2111	1283	X-RAY DIFFRACTION	100
2.2564-2.3053	0.2792	148	0.214	1246	X-RAY DIFFRACTION	100
2.3053-2.3588	0.2496	153	0.2106	1260	X-RAY DIFFRACTION	100
2.3588-2.4175	0.2803	136	0.2108	1286	X-RAY DIFFRACTION	100
2.4175-2.4826	0.2615	146	0.2055	1281	X-RAY DIFFRACTION	100
2.4826-2.5553	0.2752	113	0.2272	1315	X-RAY DIFFRACTION	100
2.5553-2.6373	0.292	154	0.2129	1267	X-RAY DIFFRACTION	100
2.6373-2.7311	0.2814	136	0.217	1287	X-RAY DIFFRACTION	100
2.7311-2.8397	0.3106	144	0.2066	1302	X-RAY DIFFRACTION	100
2.8397-2.968	0.2114	125	0.2079	1293	X-RAY DIFFRACTION	100
2.968-3.1231	0.2852	141	0.2028	1290	X-RAY DIFFRACTION	100
3.1231-3.3168	0.2013	163	0.1923	1290	X-RAY DIFFRACTION	100
3.3168-3.5697	0.1953	144	0.1762	1310	X-RAY DIFFRACTION	100
3.5697-3.9231	0.201	127	0.1548	1308	X-RAY DIFFRACTION	100
3.9231-4.4776	0.1908	154	0.1591	1314	X-RAY DIFFRACTION	100
4.4776-5.5922	0.2096	165	0.1766	1338	X-RAY DIFFRACTION	100
5.5922-14.999	0.2519	157	0.2095	1381	X-RAY DIFFRACTION	100

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	3.908	1.6606	-0.5763	1.7365	-0.7022	0.6321	-0.2573	0.3155	0.1021	0.0709	0.1623	0.0516	-0.062	-0.2409	0.1608	0.5498	-0.0003	0.0227	0.192	0.0211	0.0965	10.4328	-16.8488	5.014
2	2.2755	-1.3186	-0.5857	1.4129	-1.937	-4.6338	-0.2725	0.2468	0.1991	0.6111	0.0333	-0.1789	-0.0445	-0.209	0.1775	0.7375	0.1471	-0.0026	0.5616	-0.1392	0.103	15.1357	-25.2456	10.9653
3	1.3444	0.7018	0.5146	2.3467	-4.1758	8.6129	-0.4581	-0.4732	-0.1413	-0.4135	-0.068	-0.4907	0.8118	1.1335	0.3876	0.6985	0.1497	0.0906	0.293	0.0011	0.2555	27.8761	-31.3606	3.8735
4	2.4099	-0.2573	-0.4045	1.0726	-0.8896	-0.6711	0.4216	-0.0604	-0.4466	0.4935	-0.2298	0.0802	-0.3445	-0.1648	-0.1934	0.6695	0.0351	0.0115	0.2413	0.0376	0.1537	13.5252	-34.2081	4.8119
5	1.799	-0.2762	0.2686	1.0001	-0.4568	-0.0511	-0.004	0.0728	-0.0631	0.0886	0.0032	0.2507	0.3005	-0.0977	0.0645	0.6628	-0.0528	0.0718	0.1833	-0.0038	0.1147	7.7705	-25.1798	-0.4852
6	0.9751	0.1199	-0.4866	0.1795	-0.51	5.8789	-0.1129	0.0478	-0.049	-0.3515	0.1016	-0.1204	0.2546	-0.2889	-0.0375	0.3934	-0.0093	0.0155	0.1664	0.0016	0.1267	23.8026	-12.3227	12.3679
7	0.7588	-0.2067	0.0092	1.0162	-0.3685	-2.3194	-0.2057	-0.1188	0.0321	0.0788	0.021	-0.0158	0.5344	1.0927	-0.098	0.5904	0.0238	0.0938	0.4199	0.009	0.2548	32.9282	-16.3678	-1.1955
8	-0.6201	-0.1466	0.0007	1.2963	-1.4496	1.5449	0.1524	0.182	0.2441	-0.3514	-0.0961	-0.0176	0.2287	-0.1971	-0.0448	0.6438	0.0241	0.0763	0.1915	-0.0353	0.084	17.3882	-20.9857	-8.6388
9	3.0048	1.1837	1.073	-1.5549	1.2451	3.4343	-0.2139	0.4483	0.2119	0.3475	0.0951	0.2181	0.1986	-0.1269	0.144	0.4604	-0.0441	0.0052	0.296	0.003	0.2209	4.6193	-15.2458	-6.542
10	2.5677	3.0459	1.3146	3.275	3.399	3.3962	0.1216	-0.3506	0.8435	0.3165	-0.0651	0.5499	-0.0878	-0.4673	-0.163	0.4903	0.0308	-0.0642	0.2119	0.0591	0.2746	5.2303	-7.2116	5.2838
11	-0.176	2.1043	-0.5567	5.0492	2.171	2.678	0.135	0.0696	0.0616	0.4518	-0.0821	-0.1727	0.1774	-0.1943	-0.0623	0.0674	0.0056	-0.0464	0.1532	0.0159	0.1894	28.4907	-15.7895	-31.0387
12	0.0047	-0.8277	0.3484	1.611	1.0432	2.2352	0.1415	0.1802	-0.1654	0.4588	0.0973	0.2687	0.1413	-0.0216	-0.1161	0.1022	-0.031	0.0109	0.1766	0.0276	0.1888	22.141	-6.4381	-26.796
13	-2.2893	-1.7573	0.3543	2.842	0.4035	3.2568	0.1554	-0.0783	0.0958	-0.1017	-0.0442	0.0891	-0.1394	-0.3242	-0.0843	0.0404	0.0096	0.0174	0.1703	0.0139	0.2516	17.4867	-0.5168	-38.3429
14	2.308	4.4665	-5.7766	7.747	-0.1691	-2.5203	0.3643	-0.17	0.3366	1.0777	-0.018	0.3343	0.1047	0.5635	-0.3898	0.2052	0.0232	-0.1031	0.2842	-0.0295	0.2131	30.2391	0.7757	-24.6784
15	0.7805	-0.9516	-0.7464	0.4889	0.1639	0.0045	-0.0113	-0.1749	0.062	0.0961	-0.1052	-0.3006	-0.0439	0.0138	0.0797	0.066	-0.0355	-0.0078	0.1731	0.0069	0.2913	31.3519	-5.1159	-35.1591
16	-0.7819	-0.5086	-0.2962	2.5898	-0.3941	0.3802	0.0305	0.0163	0.0073	0.1731	-0.021	-0.0768	0.0083	-0.0204	0.0171	0.0206	-0.0288	-0.0132	0.1635	-0.0265	0.1776	23.0252	-16.6391	-33.7516
17	1.7532	-1.7431	-0.7764	4.2794	4.2785	8.2106	-0.0169	0.0988	-0.6163	0.8374	-0.219	-0.2748	0.7665	-0.2647	0.1142	0.2069	-0.0483	0.0183	0.1884	0.0191	0.1581	12.9417	-24.1572	-21.8146
18	-0.3171	1.0956	-2.4093	2.5997	-1.2456	1.7357	0.1359	0.1453	0.2696	0.3037	0.1883	0.3115	-0.2079	-0.4534	-0.1394	0.103	-0.0113	0.0237	0.2302	0.0236	0.1809	10.0448	-14.328	-25.9614
19	-1.9809	0.9121	-0.9148	2.3014	0.4203	1.5142	0.1195	0.2557	-0.0559	-0.203	0.0238	-0.1817	-0.0796	0.0358	-0.1502	0.0415	-0.0082	0.0426	0.092	-0.0002	0.179	27.012	-13.0722	-43.9458
20	-1.3463	1.8483	0.9993	1.8011	-0.4654	1.0883	-0.0261	-0.0049	-0.0583	0.3719	-0.0086	-0.468	0.157	0.2452	-0.0771	0.1154	0.0122	-0.0432	0.1668	-0.027	0.3284	31.8821	-25.7962	-30.9091

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 1:21
2	X-RAY DIFFRACTION	2	chain A and resid 22:43
3	X-RAY DIFFRACTION	3	chain A and resid 44:58
4	X-RAY DIFFRACTION	4	chain A and resid 59:75
5	X-RAY DIFFRACTION	5	chain A and resid 76:111
6	X-RAY DIFFRACTION	6	chain A and resid 112:159
7	X-RAY DIFFRACTION	7	chain A and resid 160:166
8	X-RAY DIFFRACTION	8	chain A and resid 167:183
9	X-RAY DIFFRACTION	9	chain A and resid 184:200
10	X-RAY DIFFRACTION	10	chain A and resid 201:214
11	X-RAY DIFFRACTION	11	chain B and resid 1:20
12	X-RAY DIFFRACTION	12	chain B and resid 21:44
13	X-RAY DIFFRACTION	13	chain B and resid 45:68
14	X-RAY DIFFRACTION	14	chain B and resid 69:77
15	X-RAY DIFFRACTION	15	chain B and resid 78:96
16	X-RAY DIFFRACTION	16	chain B and resid 97:135
17	X-RAY DIFFRACTION	17	chain B and resid 136:147
18	X-RAY DIFFRACTION	18	chain B and resid 148:159
19	X-RAY DIFFRACTION	19	chain B and resid 160:193
20	X-RAY DIFFRACTION	20	chain B and resid 194:214

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