PDB-5ycc: Crystal structure of Notothenia coriiceps adenylate kinase variant

ID or keywords:

Entry

Database: PDB / ID: 5ycc

Title

Crystal structure of Notothenia coriiceps adenylate kinase variant

Components

adenylate kinase

Keywords

TRANSFERASE / phosphorylation

Function / homology

Function and homology information

dAMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process / ATP binding / cytoplasm
Similarity search - Function

Biological species

Notothenia coriiceps (black rockcod)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

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

Funding support

Korea, Republic Of, 2items

Citation

Journal: To Be Published
Title: Crystal structure of Notothenia coriiceps adenylate kinase variant
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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Download

PDBx/mmCIF format	5ycc.cif.gz	163 KB	Display	PDBx/mmCIF format
PDB format	pdb5ycc.ent.gz	130.1 KB	Display	PDB format
PDBx/mmJSON format	5ycc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ycc_validation.pdf.gz	950.2 KB	Display	wwPDB validaton report
Full document	5ycc_full_validation.pdf.gz	957.2 KB	Display
Data in XML	5ycc_validation.xml.gz	16.8 KB	Display
Data in CIF	5ycc_validation.cif.gz	21.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yc/5ycc ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5ycc	HTTPS FTP

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Related structure data

Related structure data	5x6kS S: Starting model for refinement
Similar structure data	5xru-1 5x6l-1 1ivn-d 5x6l-2 5ycd-1 2ukd-d 5ycf-2 5x6k-1 5b5s-d 5xru-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

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

1

A: adenylate kinase

hetero molecules

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

2

B: adenylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.200, 105.200, 83.779
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	adenylate kinase Mass: 21313.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Notothenia coriiceps (black rockcod) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R2JFU5*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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.72 Å³/Da / Density % sol: 54.76 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.14M Lithium sulfate, 45% PEG400, 0.1M ACETATE pH4.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 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: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 13506 / % possible obs: 99.9 % / Redundancy: 16 % / R_pim(I) all: 0.036 / Net I/σ(I): 22.1
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1313 / R_pim(I) all: 0.204 / % 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: 2.7→32.347 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.27

	R_factor	Num. reflection	% reflection
R_free	0.2225	695	5.18 %
R_work	0.1679	-	-
obs	0.1709	13426	99.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→32.347 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2872	0	124	28	3024

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3040
X-RAY DIFFRACTION	f_angle_d	1.16	4106
X-RAY DIFFRACTION	f_dihedral_angle_d	14.889	1150
X-RAY DIFFRACTION	f_chiral_restr	0.04	454
X-RAY DIFFRACTION	f_plane_restr	0.005	504

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 (%)
2.6946-2.9025	0.3134	117	0.2121	2481	X-RAY DIFFRACTION	99
2.9025-3.1943	0.2486	145	0.1891	2494	X-RAY DIFFRACTION	100
3.1943-3.656	0.2416	133	0.1599	2534	X-RAY DIFFRACTION	100
3.656-4.6041	0.185	152	0.1418	2546	X-RAY DIFFRACTION	100
4.6041-32.3497	0.2155	148	0.177	2676	X-RAY DIFFRACTION	99

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	7.2361	-0.4793	1.9035	6.8028	-1.0809	4.6815	0.3215	-0.1853	0.495	0.2549	0.0767	0.1446	0.2184	-0.163	-0.1632	0.1888	-0.089	0.0574	0.3738	-0.0613	0.1909	-31.2303	-6.43	-18.2351
2	8.9096	2.5195	0.9276	2.6898	1.9363	3.7831	0.2385	0.318	0.2082	-0.2015	-0.6646	-0.7237	-0.6084	0.1664	0.2061	0.3954	-0.0245	0.1451	0.2568	-0.0114	0.4692	-27.5785	1.896	-23.063
3	4.8416	-0.3797	1.1372	9.6549	1.2259	5.9488	0.5987	0.6988	1.1021	-0.5542	-0.4869	-0.4867	-0.0998	-0.1576	-0.0091	0.2524	-0.014	0.083	0.3205	0.0439	0.3122	-20.4042	-12.6107	-25.123
4	4.5318	0.8082	-1.2337	4.4373	-0.7874	5.3328	0.3599	0.2879	-0.3858	-0.4468	-0.1038	0.0362	0.2768	-0.177	-0.2272	0.3846	0.04	0.0445	0.4143	-0.0313	0.2026	-22.1206	-24.4555	-27.2232
5	8.2564	2.0281	-0.9972	9.0582	0.7978	4.6378	0.1596	-0.3067	0.3626	-0.3241	0.0102	-1.084	-0.3328	0.4598	-0.159	0.1756	-0.0171	-0.0045	0.4345	-0.0207	0.328	-17.7976	-12.8966	-15.1129
6	7.7676	-0.9183	-0.8054	5.082	0.5503	5.5273	0.011	-0.0755	0.2652	0.4379	0.3273	-0.0785	0.0899	0.2987	-0.2327	0.2131	0.0226	0.0481	0.3415	-0.0149	0.2411	-26.5437	-11.8286	-12.7823
7	4.9935	-0.9931	1.5896	4.7046	1.5497	6.3294	0.0076	-0.9269	0.2659	-0.4471	0.0005	0.0183	-0.2448	-0.9759	-0.049	0.1698	-0.0431	0.0189	0.2327	-0.0095	0.3124	-34.8979	-6.416	-15.4219
8	5.309	-2.0432	0.3494	7.7427	0.7829	5.7276	0.3883	0.8489	-0.5989	-1.1814	-0.552	0.4007	-0.0218	0.7829	0.2425	0.3468	0.117	-0.0833	0.5016	-0.0137	0.4166	-36.5619	-16.0283	-32.8241
9	2.8887	-1.4244	0.8911	6.2406	-4.1523	5.4139	0.234	-0.1206	-0.0073	-0.1971	-0.2185	0.5077	-0.0242	-0.2049	-0.1029	0.1862	0.0295	0.0205	0.3255	-0.0719	0.2465	-39.8078	-7.2839	-15.5412
10	2.9596	0.5711	-1.0389	8.0963	3.5258	5.3665	0.2541	0.068	0.9942	0.0317	-0.3606	-0.4234	-1.9029	-0.0403	-0.0694	0.3999	0.048	0.1383	0.3015	0.0137	0.4851	-35.9503	5.5832	-20.4967
11	2.4532	-0.0971	-0.7825	1.5855	-1.6308	3.6137	0.19	-0.7402	-0.4921	0.2242	0.0205	-0.3849	-0.2078	-0.0095	-0.1759	0.2959	-0.0891	-0.0734	0.5134	0.1684	0.4088	-50.5574	-25.9895	6.8826
12	4.8932	2.3666	2.8077	2.3895	1.741	4.0642	0.3249	-0.7787	0.6547	0.1246	-0.2501	0.2506	0.4232	-0.0215	-0.1488	0.2111	-0.0541	0.0063	0.3638	0.0555	0.3111	-64.472	-23.491	1.545
13	8.6371	1.1878	-5.3418	5.4991	-0.1756	5.8204	-0.3677	0.9998	0.4039	-0.6302	0.1891	0.5621	-0.1004	0.0825	0.199	0.316	-0.0645	-0.1036	0.4599	0.1541	0.3648	-67.9034	-22.1014	-9.7187
14	6.8291	0.5614	-1.1971	6.1663	4.2812	3.4751	0.1408	-0.6638	0.6574	0.0169	-0.1696	0.3957	-0.6677	-0.9853	0.0206	0.267	-0.0079	-0.0319	0.4126	-0.0124	0.3905	-62.0006	-13.1938	1.5223
15	5.121	-0.1669	-1.2709	7.5601	-0.5903	8.8542	0.325	-0.9995	0.1154	0.6937	0.0996	0.7119	0.0242	0.3803	-0.3497	0.2504	-0.1082	0.0333	0.5482	0.1452	0.3912	-55.369	-18.1038	5.987
16	2.3847	0.6134	-3.425	9.0681	5.4081	9.3294	-0.0555	0.4768	0.9761	-0.3015	-0.28	1.242	-0.8621	-0.3881	0.2169	0.3608	0.0266	0.0321	0.3329	0.1231	0.4639	-52.6596	-9.4215	-3.7739
17	5.3861	-0.3359	-0.1267	7.4378	2.9476	4.082	0.2522	0.2128	-1.0336	-0.5811	-0.1989	-0.4207	0.3008	-0.0795	-0.1	0.2435	0.0635	-0.0693	0.3123	0.0851	0.2843	-49.5562	-31.0508	-3.4734
18	7.5758	4.6161	0.5882	6.4934	0.6254	1.4147	-0.0518	0.7247	-0.4182	-0.2519	0.0249	-0.097	0.1554	-0.1375	0.025	0.3211	0.0215	0.0122	0.4732	0.0161	0.2579	-51.6927	-26.0965	-10.1919
19	0.1565	0.3962	-0.3612	2.4002	-1.0214	0.9101	0.0722	-0.4836	-0.402	-0.2671	-0.2328	-1.2124	0.4551	0.5463	-0.0009	0.3683	-0.0079	-0.0907	0.4181	0.1509	0.5518	-40.5269	-28.7529	0.8941
20	5.8933	0.46	0.1988	3.1988	3.4754	9.1876	-0.3292	-0.9337	-0.6731	0.3404	0.1714	-0.235	-0.4868	0.0553	0.0509	0.3422	-0.0755	-0.1726	0.5682	0.2485	0.5777	-41.9523	-29.5735	9.6948

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 48 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 68 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 85 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 86 through 108 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 109 through 121 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 122 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 8 through 34 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 35 through 49 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 50 through 68 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 69 through 82 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 83 through 98 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 108 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 109 through 135 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 136 through 167 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 168 through 178 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 179 through 193 )

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