PDB-4nu0: Crystal structure of Adenylate kinase from Streptococcus pneumoni...

ID or keywords:

Entry

Database: PDB / ID: 4nu0

Title

Crystal structure of Adenylate kinase from Streptococcus pneumoniae with Ap5A

Components

Adenylate kinase

Keywords

TRANSFERASE /

adenylate kinase / capsular polysaccharide / growth / CORE / NMP/LID domain / AMP/ATP binding /

phosphotransferase

Function / homology

Function and homology information

adenylate kinase /

adenylate kinase activity / AMP salvage /

phosphorylation /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.485 Å

Authors

Thach, T.T. / Luong, T.T. / Lee, S.H. / Rhee, D.K.

Citation

Journal: FEBS Open Bio / Year: 2014
Title: Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity
Authors: Thach, T.T. / Luong, T.T. / Lee, S.H. / Rhee, D.K.

History

Deposition	Dec 3, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2014	Group: Database references
Revision 1.2	Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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	4nu0.cif.gz	268 KB	Display	PDBx/mmCIF format
PDB format	pdb4nu0.ent.gz	221.6 KB	Display	PDB format
PDBx/mmJSON format	4nu0.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/nu/4nu0 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nu0	HTTPS FTP

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Related structure data

Related structure data	4ntzSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3dkv-d 4w5j-2 4jl5-2 3dl0-1 4w5j-1 4typ-2 4typ-3 4jlo-2 5g41-d 1s3g-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) 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

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

1

A: Adenylate kinase

hetero molecules

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

2

B: Adenylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	39.202, 48.338, 52.574
Angle α, β, γ (deg.)	75.30, 72.95, 88.77
Int Tables number	1
Space group name H-M	P1

#1: Protein	Adenylate kinase / / AK / ATP-AMP transphosphorylase / ATP-AMP phosphotransferase / Adenylate monophosphate kinase Mass: 24155.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / Gene: adk, SPD_0214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04ML5, adenylate kinase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₉N₁₀O₂₂P₅
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 584 / 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: 1.94 Å³/Da / Density % sol: 36.47 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate, 0.1M sodium acetate pH 4.6, 30% PEG 8K, 50mM NaF, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection	Resolution: 1.48→50 Å / Num. all: 54770 / Num. obs: 54770 / % possible obs: 93.11 % / Redundancy: 3.7 % / R_merge(I) obs: 0.061
Reflection shell	Resolution: 1.48→1.51 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 5.97 / % possible all: 87.46

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Processing

Software

Name	Version	Classification
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASES		phasing
PHENIX	dev_1555	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4NTZ

4ntz

Resolution: 1.485→37.418 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / σ(F): 1.98 / Phase error: 27.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2299	1997	3.65 %
R_work	0.1934	-	-
obs	0.1947	54726	93.04 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 40.9085 Å²

Refinement step

Cycle: LAST / Resolution: 1.485→37.418 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3336	0	116	584	4036

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3512
X-RAY DIFFRACTION	f_angle_d	0.94	4772
X-RAY DIFFRACTION	f_dihedral_angle_d	14.05	1356
X-RAY DIFFRACTION	f_chiral_restr	0.045	534
X-RAY DIFFRACTION	f_plane_restr	0.003	610

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 (%)
1.4855-1.5226	0.2997	129	0.2581	3443	X-RAY DIFFRACTION	84
1.5226-1.5638	0.338	146	0.2372	3812	X-RAY DIFFRACTION	94
1.5638-1.6098	0.2752	143	0.2262	3813	X-RAY DIFFRACTION	94
1.6098-1.6617	0.2836	147	0.2144	3860	X-RAY DIFFRACTION	95
1.6617-1.7211	0.2585	144	0.2097	3835	X-RAY DIFFRACTION	95
1.7211-1.79	0.2467	148	0.2063	3886	X-RAY DIFFRACTION	96
1.79-1.8715	0.253	148	0.2098	3902	X-RAY DIFFRACTION	96
1.8715-1.9702	0.2705	146	0.1997	3860	X-RAY DIFFRACTION	96
1.9702-2.0936	0.232	147	0.1898	3897	X-RAY DIFFRACTION	97
2.0936-2.2552	0.215	149	0.181	3894	X-RAY DIFFRACTION	96
2.2552-2.4821	0.1918	146	0.184	3889	X-RAY DIFFRACTION	96
2.4821-2.8412	0.2576	146	0.1895	3851	X-RAY DIFFRACTION	95
2.8412-3.5792	0.2073	134	0.1883	3530	X-RAY DIFFRACTION	88
3.5792-37.4294	0.2011	124	0.1855	3257	X-RAY DIFFRACTION	80

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	4.5936	4.1772	1.6586	4.1589	2.3951	2.8096	0.1748	-0.328	0.1909	0.2091	-0.235	0.2916	-0.0694	-0.0608	0.0726	0.2204	0.003	0.0538	0.2348	-0.0104	0.335	-8.8545	6.5139	70.3597
2	7.9559	3.5933	1.7524	2.3252	2.2132	3.2774	-0.1142	0.5529	0.7354	-0.6267	0.0959	-0.1373	-0.5909	-0.0977	0.2341	0.3857	0.0226	0.0994	0.2652	0.0027	0.3966	-10.6219	12.0927	60.927
3	2.8577	-4.4037	-2.083	6.7492	3.1464	5.7542	0.2739	0.28	0.0942	-0.4086	-0.1159	0.1972	-0.3295	0.0203	-0.1219	0.2522	-0.0022	0.0576	0.2872	-0.0324	0.373	1.6717	2.2281	61.9328
4	6.7042	4.961	-5.4601	3.788	-4.002	5.856	0.0951	0.2528	0.1724	-0.2277	0.0427	0.1305	0.171	0.1143	-0.0442	0.2706	0.0296	0.0594	0.327	-0.039	0.4192	8.4556	-6.9641	62.0116
5	1.7142	0.9309	-0.9687	9.2906	0.3681	1.065	-0.1269	-0.2606	-0.0413	0.6624	0.4019	-0.616	-0.0004	0.371	-0.0951	0.2502	0.0458	-0.0092	0.3851	-0.0347	0.3622	6.4621	1.0055	70.8212
6	3.0402	-2.7869	0.7875	6.3451	-1.8748	3.5071	0.1389	0.1717	0.3991	0.1684	0.0165	-0.4699	-0.5419	0.394	-0.0651	0.3343	-0.0522	0.0795	0.2933	-0.0673	0.3597	1.0264	12.6413	68.6984
7	3.5239	2.6629	-0.2509	2.2348	-0.4172	5.0769	0.2254	-0.4734	0.0605	0.4462	-0.1916	-0.2826	0.0719	0.9839	-0.0602	0.3155	-0.0072	0.0178	0.4276	-0.079	0.3644	3.5248	7.9652	79.7991
8	2.6571	1.0128	0.0717	2.0862	1.4539	2.4891	-0.0667	0.0239	-0.0163	-0.1513	-0.0379	0.0481	-0.1371	-0.0063	0.1542	0.246	0.0127	0.0547	0.2066	0.0048	0.3364	-11.3496	0.9009	63.6004
9	7.3872	-0.8602	-0.3494	3.442	1.8756	4.7212	0.2544	1.1996	-0.3457	-0.664	-0.0993	0.158	-0.2292	0.0705	-0.039	0.3878	0.0096	0.0754	0.3359	-0.0699	0.373	-11.4927	-4.9779	50.1948
10	1.3773	-0.6903	-0.2248	2.6637	1.5208	1.636	-0.0339	-0.2084	-0.1768	0.3154	-0.0599	0.0089	0.2533	0.0088	-0.0115	0.2988	-0.0339	0.0833	0.2972	0.0339	0.352	-10.7596	-1.2042	74.935
11	3.4681	3.291	3.6758	4.0745	5.3109	7.2655	-0.0898	-0.1605	0.5434	-0.515	-0.3111	0.7596	-0.552	-0.3217	0.2121	0.3195	0.0463	0.0298	0.2603	-0.0568	0.4224	-18.6051	13.9607	66.4111
12	7.53	6.1313	1.3129	5.6691	2.3608	2.8736	0.3238	-1.1071	0.0021	0.2239	-0.4369	0.713	-0.004	-0.1753	0.0976	0.1993	-0.0058	0.0395	0.3651	0.0381	0.3982	18.999	36.317	94.6507
13	7.8508	4.6868	-1.0575	3.2571	0.6273	5.1467	-0.0348	0.0628	0.6069	-0.307	0.0167	0.0013	-0.5715	-0.1174	0.2623	0.2795	-0.0029	0.0432	0.221	-0.0307	0.3528	16.4469	42.5425	85.9383
14	7.1588	-2.0287	-0.8963	3.348	1.6038	3.5787	0.17	0.269	-0.3821	-0.1425	-0.1633	0.172	-0.2826	0.0259	-0.1118	0.236	0.0045	0.0209	0.2381	-0.0247	0.3417	29.502	32.608	85.8753
15	8.7457	5.5118	-2.9873	5.5462	-1.6195	1.1123	-0.2506	0.5735	-0.2093	-0.0565	0.2181	-0.0043	0.1612	-0.1229	0.0357	0.2523	-0.0114	0.0524	0.2557	-0.0141	0.4777	36.2624	23.6249	85.4026
16	2.2397	0.4256	-1.1554	6.6945	0.2816	0.9274	-0.109	-0.2398	-0.3915	0.2327	0.2546	-0.5272	0.0878	0.2739	0.0723	0.2464	0.0117	0.0049	0.2911	0.0239	0.3559	34.1806	31.2181	94.8414
17	5.4093	-0.6278	0.7235	6.6604	-3.876	7.8291	0.1005	-0.1654	0.395	0.1966	-0.0157	0.0659	-0.5963	0.2023	-0.123	0.2537	-0.0047	0.0745	0.2663	-0.0763	0.2713	28.2103	42.0607	92.7525
18	5.4602	3.517	-0.5898	2.4677	-0.3264	4.7652	0.1071	-0.6534	-0.2027	0.6735	-0.1065	-0.39	0.0609	0.3485	-0.2808	0.3004	0.0553	0.0214	0.4718	-0.0056	0.3439	31.6036	36.571	103.965
19	3.9128	0.6369	0.1864	1.8566	1.8422	2.8039	-0.0999	-0.4285	-0.3383	-0.0678	-0.0869	0.0548	-0.0668	-0.0387	0.0988	0.2295	0.0168	0.0545	0.2325	0.0583	0.3717	16.4698	31.2074	87.7348
20	3.4212	0.0413	-0.7299	3.269	-0.0438	5.3345	0.2098	0.7254	-0.417	-0.5315	-0.2237	0.0646	0.0485	0.112	-0.0706	0.3062	0.0335	0.0246	0.2535	-0.0658	0.3957	16.5523	26.2094	74.0491
21	0.816	0.4313	-0.1151	9.7568	7.5187	7.846	0.1074	-0.4141	-0.3802	0.7838	-0.1682	0.0601	0.6562	-0.2322	0.0151	0.2941	-0.0095	0.0648	0.3463	0.0805	0.4247	20.3006	22.9878	97.7851
22	1.6168	0.3427	3.7973	2.2149	1.9375	9.3975	0.1235	-0.783	-0.2178	0.2339	0.0298	0.1404	0.1306	-0.3414	-0.0989	0.2417	-0.0479	0.082	0.6302	-0.0221	0.2852	11.3855	37.0551	99.6389
23	3.7663	1.5253	1.514	4.444	2.6892	4.0302	-0.0337	-0.4895	0.5132	0.0033	-0.2651	0.4623	-0.3274	-0.4108	0.2175	0.2482	0.0354	0.057	0.2789	-0.0917	0.3398	8.961	43.8592	91.4774

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:12 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 13:26 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 27:40 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 41:55 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 56:72 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 73:90 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 91:104 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 105:139 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 140:160 )
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 161:196 )
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESID 197:212 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 1:12 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 13:26 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 27:40 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 41:55 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 56:73 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 74:90 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 91:104 )
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 105:139 )
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESID 140:160 )
21	X-RAY DIFFRACTION	21	CHAIN B AND (RESID 161:183 )
22	X-RAY DIFFRACTION	22	CHAIN B AND (RESID 184:196 )
23	X-RAY DIFFRACTION	23	CHAIN B AND (RESID 197:212 )

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