PDB-3l0s: Crystal structures of Zinc, Cobalt and Iron containing Adenylate ...

ID or keywords:

Entry

Database: PDB / ID: 3l0s

Title

Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas

Components

Adenylate kinase

Keywords

TRANSFERASE /

Adenylate kinase /

Gram-negative /

Cobalt / ATP-binding /

Kinase / Nucleotide-binding

Function / homology

Function and homology information

adenylate kinase /

adenylate kinase activity / AMP salvage /

phosphorylation /

ATP binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Desulfovibrio gigas (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Mukhopadhyay, A. / Trincao, J. / Romao, M.J.

Citation

Journal: J.Biol.Inorg.Chem. / Year: 2011
Title: Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria
Authors: Mukhopadhyay, A. / Kladova, A.V. / Bursakov, S.A. / Gavel, O.Y. / Calvete, J.J. / Shnyrov, V.L. / Moura, I. / Moura, J.J.G. / Romao, M.J. / Trincao, J.

History

Deposition	Dec 10, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 15, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _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	3l0s.cif.gz	187.1 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l0/3l0s ftp://data.pdbj.org/pub/pdb/validation_reports/l0/3l0s	HTTPS FTP

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Related structure data

Related structure data	2xb4C 3l0pC C: citing same article (ref.)
Similar structure data	6ccf-2 4jwy-d 6lyv-4 3k93-d 2oid-2 4ls3-2 4beg-d 4cnh-1 5p85-d 4mxx-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
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Adenylate kinase

C: Adenylate kinase

hetero molecules

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

1

A: Adenylate kinase

hetero molecules

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

2

C: Adenylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	131.430, 39.490, 94.200
Angle α, β, γ (deg.)	90.000, 109.310, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Adenylate kinase / Mass: 24544.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio gigas (bacteria) / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: C7U112, adenylate kinase
#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.35 Å³/Da / Density % sol: 47.66 % / Mosaicity: 0.874 °
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M tartrate Na/K, 0.1 M MES (pH 6.5) and 20% PEG 2K, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 1.6064 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2007

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.6064 Å / Relative weight: 1

Reflection

Resolution: 2→88.891 Å / Num. all: 30472 / Num. obs: 30472 / % possible obs: 97.2 % / Redundancy: 3.5 % / R_merge(I) obs: 0.076 / R_pim(I) all: 0.056 / R_rim(I) all: 0.105 / R_sym value: 0.076 / Net I/av σ(I): 7.365 / Net I/σ(I): 13.3 / Num. measured all: 105651

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) all	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2-2.11	3.5	0.606	0.426	1.7	14814	4280	0.32	0.61	0.426	2.1	94.6
2.11-2.24	3.5	0.387	0.273	2.6	14265	4117	0.2	0.39	0.273	3.5	95.9
2.24-2.39	3.5	0.267	0.192	2.4	13727	3912	0.14	0.27	0.192	5.4	96.6
2.39-2.58	3.5	0.194	0.138	5.2	12850	3647	0.1	0.19	0.138	8	97
2.58-2.83	3.5	0.139	0.099	7.3	12025	3402	0.07	0.14	0.099	11.5	97
2.83-3.16	3.5	0.096	0.068	9.9	10743	3089	0.05	0.1	0.068	16.7	98.9
3.16-3.65	3.4	0.076	0.053	11.3	9507	2774	0.04	0.08	0.053	23.2	98.7
3.65-4.47	3.2	0.053	0.039	12.2	7608	2346	0.03	0.05	0.039	30	99.2
4.47-6.32	3.5	0.045	0.031	17.7	6510	1843	0.02	0.05	0.031	35.3	99.4
6.32-44.46	3.4	0.047	0.032	14.4	3602	1062	0.03	0.05	0.032	37.2	99.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 35.92

	Highest resolution	Lowest resolution
Rotation	2 Å	44.44 Å
Translation	2 Å	44.44 Å

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 30458

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.16-100	31.1	0.638	510
6.42-8.16	36.9	0.859	515
5.52-6.42	30.3	0.879	554
4.92-5.52	27.5	0.891	612
4.48-4.92	27.7	0.904	703
4.14-4.48	26.3	0.912	750
3.87-4.14	27.5	0.904	788
3.64-3.87	29.8	0.902	862
3.45-3.64	28.1	0.895	912
3.29-3.45	30.6	0.893	921
3.15-3.29	30.4	0.889	1006
3.02-3.15	32.6	0.876	1023
2.91-3.02	30.6	0.87	1062
2.81-2.91	32.2	0.867	1113
2.72-2.81	35	0.863	1116
2.64-2.72	35.8	0.868	1146
2.57-2.64	32	0.888	1187
2.5-2.57	31.9	0.883	1249
2.43-2.5	34.9	0.884	1228
2.37-2.43	32.6	0.896	1272
2.32-2.37	33.2	0.905	1325
2.27-2.32	35	0.89	1315
2.22-2.27	33.7	0.906	1357
2.17-2.22	32.1	0.905	1425
2.13-2.17	34.7	0.892	1386
2.09-2.13	35.8	0.871	1450
2.05-2.09	40.8	0.871	1424
2-2.05	44.1	0.836	2247

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.25	data scaling
PHASER	2.1	phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
DNA		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→44.46 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.91 / WR_factor R_free: 0.245 / WR_factor R_work: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.826 / SU B: 10.928 / SU ML: 0.137 / SU R Cruickshank DPI: 0.201 / SU R_free: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.254	1538	5 %	RANDOM
R_work	0.19	-	-	-
obs	0.193	30458	97.15 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 43.91 Å² / B_iso mean: 25.163 Å² / B_iso min: 2.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	-0.02 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3397	0	22	302	3721

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	3480
X-RAY DIFFRACTION	r_angle_refined_deg	1.902	1.971	4695
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.069	5	446
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.994	24.875	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.778	15	602
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.444	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.141	0.2	517
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	2653
X-RAY DIFFRACTION	r_mcbond_it	0.985	1.5	2197
X-RAY DIFFRACTION	r_mcangle_it	1.677	2	3497
X-RAY DIFFRACTION	r_scbond_it	3.23	3	1283
X-RAY DIFFRACTION	r_scangle_it	5.078	4.5	1197

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	102	-
R_work	0.3	2042	-
all	-	2144	-
obs	-	-	93.95 %

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	0.2919	-0.2854	0.1652	2.0395	0.4647	0.4174	0.0451	-0.0054	0.029	-0.2908	-0.0198	0.1627	-0.1053	-0.1062	-0.0253	0.0808	0.0073	-0.0095	0.1046	0.0395	0.1003	-25.7616	-20.9314	9.5688
2	-1.3807	-0.1584	-2.8762	5.5302	1.7722	6.3633	-0.0078	-0.0401	-0.0158	-0.2802	0.3981	0.1505	-0.3939	0.287	-0.3903	0.0555	-0.0011	0.0947	0.0868	0.047	0.1206	-24.3242	-11.3648	11.9977
3	4.313	-1.635	-0.185	2.2379	-0.9343	1.427	0.0019	-0.0498	0.0435	0.0241	0.0698	0.0998	-0.038	-0.0079	-0.0717	0.0848	-0.0322	-0.001	0.1017	-0.0039	0.0974	-12.675	-7.7741	27.8629
4	7.1988	-2.505	6.6145	3.6608	-4.5841	13.1093	0.0143	-0.0789	0.821	0.0631	-0.1005	-0.0043	-0.4048	-0.3074	0.0862	0.0232	0.0143	0.0363	0.0844	-0.0259	0.1679	-25.0819	-8.2836	22.975
5	2.8797	-2.0918	0.113	2.6808	-0.1127	1.5633	0.0491	0.0756	0.2119	0.0562	-0.0737	-0.0736	-0.0921	-0.0004	0.0246	0.07	-0.0266	0.0054	0.1156	0.0279	0.1268	-25.7002	-17.7093	22.031
6	1.8238	0.1362	0.015	2.0672	1.5535	3.1285	0.026	-0.1587	0.2176	0.0815	-0.1015	0.0916	0.014	-0.2732	0.0756	0.0274	0.0088	0.0255	0.099	0.0338	0.1106	-32.8309	-19.2553	20.5965
7	1.2962	1.0539	-3.3891	3.2854	-1.4756	4.9257	-0.0561	-0.0698	-0.0183	-0.1537	0.0428	-0.0818	0.2426	0.0199	0.0133	0.0909	0.0092	-0.0175	0.1031	-0.0051	0.0647	-14.3052	-33.0388	5.9255
8	0.9277	0.036	0.0813	0.3771	-0.8319	2.6437	0.0134	-0.0327	-0.0049	-0.0148	-0.0027	-0.0153	0.1794	0.0997	-0.0107	0.091	0.0117	-0.0061	0.0691	-0.0047	0.0695	-9.8842	-27.5786	-4.3215
9	3.145	-0.4968	0.4091	0.9102	0.1599	0.7054	0.069	0.0504	0.1421	0.0348	-0.0394	0.0417	0.0186	-0.0668	-0.0296	0.1024	-0.0168	-0.0027	0.0935	0.0233	0.0882	-26.9042	-28.8	19.352
10	7.7685	-3.5416	-2.125	9.4912	5.5989	11.0777	0.183	0.3666	-0.5285	-0.4485	-0.4527	0.689	-0.1187	-0.5601	0.2697	0.1396	-0.0732	-0.0942	0.0928	0.0013	0.0322	-31.9934	-25.8042	2.0845
11	1.0821	-0.3819	0.5288	1.9608	-1.1404	1.9946	0.0505	-0.0167	-0.1798	-0.0862	-0.07	-0.0228	0.1028	0.1679	0.0195	0.0829	-0.0142	-0.0056	0.1008	0.0003	0.0964	16.8033	-19.2512	22.4526
12	4.0493	1.7255	-4.7684	0.7469	0.4536	5.8752	-0.0749	-0.1225	0.1194	-0.1383	-0.0837	0.1238	0.2253	-0.1788	0.1586	0.1173	0.0235	-0.0219	0.0546	0.0488	0.0898	10.3362	-28.156	24.2279
13	4.6996	-1.0158	1.5113	3.1639	-1.2355	2.2807	-0.1644	0.031	0.039	0.0803	0.1367	0.034	0.0339	-0.0791	0.0277	0.1004	-0.0481	-0.0134	0.1009	-0.0251	0.0531	-5.913	-30.9313	30.0657
14	3.999	0.3633	-3.8564	2.4098	0.112	4.0688	-0.037	-0.3176	-0.3121	-0.1684	-0.0027	-0.1234	0.3789	0.1757	0.0397	0.1735	-0.0413	-0.074	0.1153	0.0325	0.1029	9.5972	-28.9298	31.925
15	4.3483	-3.0797	4.0872	5.194	-4.72	5.8366	-0.0278	-0.3047	-0.1263	0.108	0.072	0.1568	0.0458	-0.0337	-0.0442	0.095	-0.0098	0.003	0.1287	-0.0058	0.0883	6.0385	-19.8256	37.5997
16	2.2901	-0.7715	0.2456	0.623	-1.1106	1.7531	0.0938	-0.1301	-0.0174	0.019	-0.042	0.048	0.0431	0.1376	-0.0518	0.1184	-0.0004	-0.0178	0.0774	-0.0282	0.061	15.3395	-13.693	28.9148
17	2.3399	-0.2108	-0.9374	1.0942	1.1405	3.9334	0.0449	0.0013	0.0914	-0.1349	-0.0394	-0.0262	-0.1354	-0.0325	-0.0055	0.1024	0.0095	0.0072	0.0794	0.0236	0.0787	12.2177	-9.9657	4.6139
18	2.156	-0.5733	-2.3632	0.8	0.7819	3.2181	0.1102	-0.0132	0.0346	-0.1761	-0.0156	-0.0167	-0.1405	-0.1645	-0.0946	0.0894	0.0152	-0.002	0.0951	0.0052	0.0504	7.2245	-10.9334	2.6611
19	2.2055	-0.5362	0.6927	0.7989	-0.1069	1.1665	0.0698	-0.0944	-0.0232	0.0947	-0.0337	-0.0053	0.0323	0.0236	-0.036	0.0813	-0.0234	-0.0049	0.0899	-0.0138	0.0751	9.663	-10.092	31.9977
20	2.849	1.7451	-0.5822	3.7125	-0.4953	6.5496	0.0551	0.0195	0.0163	0.0234	-0.0508	0.0062	-0.1079	0.2245	-0.0043	0.0419	-0.0331	0.0246	0.1384	0.0037	0.1049	24.1357	-12.3509	20.9835

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 36
3	X-RAY DIFFRACTION	3	A	37 - 63
4	X-RAY DIFFRACTION	4	A	64 - 76
5	X-RAY DIFFRACTION	5	A	77 - 96
6	X-RAY DIFFRACTION	6	A	97 - 113
7	X-RAY DIFFRACTION	7	A	114 - 126
8	X-RAY DIFFRACTION	8	A	127 - 172
9	X-RAY DIFFRACTION	9	A	173 - 207
10	X-RAY DIFFRACTION	10	A	208 - 223
11	X-RAY DIFFRACTION	11	C	1 - 23
12	X-RAY DIFFRACTION	12	C	24 - 36
13	X-RAY DIFFRACTION	13	C	37 - 62
14	X-RAY DIFFRACTION	14	C	63 - 84
15	X-RAY DIFFRACTION	15	C	85 - 103
16	X-RAY DIFFRACTION	16	C	104 - 116
17	X-RAY DIFFRACTION	17	C	117 - 146
18	X-RAY DIFFRACTION	18	C	147 - 172
19	X-RAY DIFFRACTION	19	C	173 - 203
20	X-RAY DIFFRACTION	20	C	204 - 223

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi