PDB-5ycd: Crystal structure of Poecilia reticulata adenylate kinase

ID or keywords:

Entry

Database: PDB / ID: 5ycd

Title

Crystal structure of Poecilia reticulata adenylate kinase

Components

Adenylayte kinase

Keywords

TRANSFERASE /

phosphorylation

Function / homology

Function and homology information

AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process /

adenylate kinase /

adenylate kinase activity /

nucleoside-diphosphate kinase /

nucleoside diphosphate kinase activity / ATP metabolic process /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Poecilia reticulata (guppy)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Bae, E. / Kim, J. / Moon, S.

Funding support

Korea, Republic Of, 2items

Citation

Journal: To Be Published
Title: Crystal structure of Poecilia reticulata adenylate kinase
Authors: Bae, E. / Kim, J. / Moon, S.

History

Deposition	Sep 7, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 19, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2	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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PDBx/mmCIF format	5ycd.cif.gz	172.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ycd.ent.gz	136.3 KB	Display	PDB format
PDBx/mmJSON format	5ycd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yc/5ycd ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5ycd	HTTPS FTP

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Related structure data

Related structure data	5x6kS S: Starting model for refinement
Similar structure data	5ycf-2 5ycf-1 5xru-1 5xz2-1 1uky-d 3uy9-15 5x6l-2 5xz2-2 5gib-2 5ycb-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) 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: Adenylayte kinase

B: Adenylayte kinase

hetero molecules

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

1

A: Adenylayte kinase

hetero molecules

defined by author&software
Evidence: gel filtration, monomeric
22.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Adenylayte kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	40.790, 81.505, 120.123
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Adenylayte kinase Mass: 21181.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Poecilia reticulata (guppy) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSM2*PLUS
#2: Chemical	ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₉N₁₀O₂₂P₅
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.36 Å³/Da / Density % sol: 47.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 27.5% PEG3350, 0.1M Citric acid

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979933 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 29, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979933 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 37999 / % possible obs: 99.9 % / Redundancy: 14.2 % / R_pim(I) all: 0.027 / Net I/σ(I): 28.01
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 5.13 / Num. unique obs: 3759 / R_pim(I) all: 0.193 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5X6K

5x6k

Resolution: 1.8→31.178 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.33

	R_factor	Num. reflection	% reflection
R_free	0.2091	1896	5 %
R_work	0.1665	-	-
obs	0.1686	37930	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→31.178 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2953	0	116	309	3378

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3111
X-RAY DIFFRACTION	f_angle_d	1.193	4195
X-RAY DIFFRACTION	f_dihedral_angle_d	12.841	1177
X-RAY DIFFRACTION	f_chiral_restr	0.041	468
X-RAY DIFFRACTION	f_plane_restr	0.004	516

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 (%)
1.7998-1.8448	0.255	130	0.2023	2475	X-RAY DIFFRACTION	97
1.8448-1.8947	0.2668	133	0.1991	2533	X-RAY DIFFRACTION	100
1.8947-1.9505	0.2546	134	0.201	2550	X-RAY DIFFRACTION	100
1.9505-2.0134	0.1974	134	0.1824	2526	X-RAY DIFFRACTION	100
2.0134-2.0853	0.2186	134	0.1822	2544	X-RAY DIFFRACTION	100
2.0853-2.1688	0.2289	134	0.1786	2564	X-RAY DIFFRACTION	100
2.1688-2.2675	0.2129	134	0.1707	2562	X-RAY DIFFRACTION	100
2.2675-2.387	0.2155	134	0.1708	2542	X-RAY DIFFRACTION	100
2.387-2.5365	0.2328	135	0.1828	2570	X-RAY DIFFRACTION	100
2.5365-2.7322	0.2422	137	0.1792	2580	X-RAY DIFFRACTION	100
2.7322-3.007	0.2325	135	0.1815	2569	X-RAY DIFFRACTION	100
3.007-3.4416	0.2111	138	0.1622	2617	X-RAY DIFFRACTION	100
3.4416-4.3342	0.1699	138	0.1395	2637	X-RAY DIFFRACTION	100
4.3342-31.1822	0.1839	146	0.1514	2765	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	5.4022	-1.9962	0.0384	4.8074	-1.0729	2.3876	0.0177	0.0374	-0.5917	-0.1916	0.2774	-0.4409	0.7858	0.2204	-0.0355	0.3526	0.0719	-0.0662	0.1861	-0.076	0.2293	-7.5275	-8.7438	-20.7009
2	6.7379	1.5727	-0.984	1.7585	-0.3832	1.9979	0.2513	-0.4469	-0.1307	0.2109	-0.1486	-0.04	0.2033	0.0866	-0.1228	0.219	0.0148	-0.0277	0.1846	-0.0179	0.1067	-7.5419	-2.6704	-11.7914
3	4.8471	-4.5395	4.2276	4.7011	-3.6949	4.7647	0.0924	-0.0548	1.0946	0.053	0.0325	-0.2939	-0.4477	0.8571	0.0913	0.1496	-0.0315	0.0132	0.3169	-0.0891	0.3096	6.8147	11.1847	-16.3288
4	2.0618	-1.7772	0.2579	8.0662	-3.1017	3.8246	-0.0381	-0.1654	0.0092	-0.2053	0.0276	-0.9503	0.5153	0.6119	0.0931	0.2073	0.1167	-0.0384	0.3185	-0.059	0.2447	3.1064	-2.1371	-20.6129
5	4.3638	-1.7406	1.4933	3.6402	-5.4455	8.5343	0.1657	-0.1568	-0.2195	-0.5016	0.0822	0.2491	0.8325	0.1534	-0.1465	0.2848	0.0396	-0.0583	0.1542	-0.0453	0.1423	-4.8891	-7.4474	-18.3275
6	4.1825	-0.8079	-0.6811	5.0981	0.7413	4.5616	0.0091	0.2935	-0.222	-0.1777	0.0081	-0.2348	0.4446	0.1863	0.0095	0.2102	0.0268	-0.0518	0.1623	-0.0289	0.0672	-7.8338	-4.9178	-26.975
7	5.7488	5.5598	3.0901	8.458	4.3042	2.7713	0.0839	0.1698	0.07	0.2269	0.0278	-0.0318	-0.2972	0.2395	-0.1473	0.1978	0.0489	0.0307	0.2061	0.0197	0.156	-13.2572	14.474	-13.0192
8	6.1409	1.3267	1.8034	7.7483	4.4737	2.794	-0.1608	0.2981	0.8411	-0.8006	0.077	-0.3056	-0.7314	-0.0183	0.0269	0.3084	0.0455	0.0115	0.2313	0.0836	0.2735	-10.1156	14.2207	-24.5698
9	1.8944	-0.0058	-0.8314	1.087	0.671	3.5241	0.1112	0.1701	0.0911	-0.2334	-0.117	0.2371	0.0342	-0.4432	0.0301	0.201	-0.0018	-0.05	0.2729	-0.0324	0.1376	-17.0856	-2.1923	-26.8735
10	3.8071	-5.1356	-2.0644	7.6297	1.36	4.3021	0.1068	-0.1798	-0.3412	0.0262	0.0691	0.4522	0.7205	-0.6648	-0.1716	0.2659	-0.0996	-0.0345	0.3236	0.0281	0.2002	-22.2117	-8.1689	-15.2287
11	6.2961	4.944	0.8103	6.2107	0.1789	2.4989	-0.05	0.0281	-0.0169	-0.2266	0.0785	-0.2127	-0.466	0.0822	-0.0131	0.2436	-0.0374	0.0054	0.1872	0.0178	0.1402	-0.7803	8.3108	8.383
12	3.8935	-0.8486	0.3566	2.4886	0.2879	2.0311	0.2029	0.2521	-0.5432	-0.1	-0.0855	-0.1241	0.1199	0.1919	-0.1175	0.1454	-0.0116	-0.0316	0.1567	-0.0418	0.186	3.0123	-3.8961	2.0422
13	4.3497	1.1851	0.0447	7.6565	-2.2595	4.6041	0.0627	0.0132	-0.2495	-0.0224	-0.0298	-0.4031	-0.2049	0.2796	-0.0086	0.1276	-0.0413	-0.0024	0.1552	-0.0479	0.1317	5.2871	2.7766	8.0029
14	1.7536	0.3044	0.7506	4.1849	1.6152	2.7935	0.1315	-0.0344	-0.2977	0.0469	-0.0778	0.0161	0.1797	0.01	-0.05	0.1496	-0.0224	-0.0047	0.1778	0.0686	0.1215	-4.7325	-5.3911	9.0598
15	5.1832	-3.2767	-3.9053	7.6557	2.1231	8.2381	-0.0928	-0.1875	-0.7119	0.5823	-0.0947	0.0068	1.1426	-0.2217	0.2309	0.3597	-0.1329	-0.0557	0.2644	0.1493	0.3224	-4.535	-15.1692	13.9778
16	3.6046	-0.373	2.0604	1.7126	0.2752	5.1809	0.1332	-0.1114	-0.3297	0.1442	-0.1194	0.389	-0.1481	-0.5903	-0.0149	0.1377	0.0166	0.021	0.2384	-0.0088	0.2029	-13.5443	3.4622	10.5267

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 63 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 83 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 98 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 99 through 121 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 122 through 142 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 143 through 156 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 157 through 178 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 179 through 193 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 20 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 21 through 63 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 64 through 98 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 99 through 142 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 143 through 156 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 157 through 193 )

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