PDB-3lw7: The Crystal Structure of an Adenylate kinase-related protein boun...

ID or keywords:

Entry

Database: PDB / ID: 3lw7

Title

The Crystal Structure of an Adenylate kinase-related protein bound to AMP from sulfolobus solfataricus to 2.3A

Components

Adenylate kinase related protein (AdkA-like)

Keywords

TRANSFERASE /

adenylate /

kinase / AMP /

sulfolobus / solfataricus / PSI / MCSG /

Structural Genomics / Midwest Center for Structural Genomics /

Protein Structure Initiative / ATP-binding / Nucleotide-binding

Function / homology

Function and homology information

kinase activity /

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3 Å

Authors

Stein, A.J. / Sather, A. / Hendricks, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of an Adenylate kinase-related protein bound to AMP from sulfolobus solfataricus to 2.3A
Authors: Stein, A.J. / Sather, A. / Hendricks, R. / Abdullah, J. / Joachimiak, A.

History

Deposition	Feb 23, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	3lw7.cif.gz	152.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3lw7.ent.gz	121.7 KB	Display	PDB format
PDBx/mmJSON format	3lw7.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/lw/3lw7 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/3lw7	HTTPS FTP

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Related structure data

Similar structure data	1wq4-d 3h0k-d 1wmk-4 5cg9-2 4asx-1 5btb-d 7jhi-3 1wmk-6 5xu8-d 3sq5-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC89436

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Adenylate kinase related protein (AdkA-like)

B: Adenylate kinase related protein (AdkA-like)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.876, 65.876, 206.239
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Adenylate kinase related protein (AdkA-like) Mass: 20555.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2, 98/2 / Gene: SSO1041, Ssol_2012 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0KU01, UniProt: Q97Z90*PLUS
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.69 Å³/Da / Density % sol: 54.4 %
Crystal grow	Temperature: 277 K / pH: 4.2 Details: 10% PEG 3000, 0.1M Phosphate-citrate, pH 4.2, 0.2M Sodium chloride, vapor diffusion, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2009
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 21055 / % possible obs: 99 % / Redundancy: 6.7 % / R_merge(I) obs: 0.109 / Net I/σ(I): 7.9
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.737 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
PHASER		phasing

Refinement

Resolution: 2.3→40.6 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.924 / SU B: 12.582 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.247	1080	5.1 %	RANDOM
R_work	0.206	-	-	-
obs	0.208	20987	99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.31 Å²

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

Refinement step

Cycle: LAST / Resolution: 2.3→40.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2638	0	23	82	2743

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	2694
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.367	2.002	3627
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.314	5	341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.054	22.336	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.715	15	506
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.616	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	428
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1937
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.596	1.5	1691
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.119	2	2710
X-RAY DIFFRACTION	r_scbond_it	1.722	3	1003
X-RAY DIFFRACTION	r_scangle_it	2.925	4.5	915
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	77	-
R_work	0.243	1429	-
obs	-	-	97.86 %

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	1.5489	1.2203	-0.7335	1.3596	0.9654	3.1063	0.1094	-0.0395	-0.0299	0.0963	-0.1192	-0.0331	-0.1107	-0.0847	0.0098	0.2606	0.0179	-0.0302	0.2471	0.0416	0.1982	10.559	-15.0813	-9.6901
2	1.1943	2.2339	-0.2736	15.0177	6.7031	16.398	0.0706	0.153	0.1622	0.1183	0.012	-0.3994	-0.8058	0.8227	-0.0826	0.2835	-0.0674	-0.0169	0.3016	0.0362	0.2465	15.4574	-7.6051	-9.5749
3	1.8035	-2.1499	-3.0647	8.3769	-2.7635	6.2985	-0.0121	-0.5425	0.3048	-0.199	-0.2071	-0.7223	-0.4054	0.6589	0.2192	0.2674	0.0022	-0.0944	0.341	-0.0895	0.3091	16.4786	-11.9627	-1.2439
4	24.4751	2.0293	-1.9095	21.6616	5.3349	14.327	-0.5072	-1.8385	0.1434	-1.5066	-0.1458	-0.8837	0.3269	1.1844	0.653	0.0631	0.2341	0.1225	0.7515	0.2532	0.2114	25.3295	-25.1817	4.2196
5	8.7174	4.9174	1.8809	10.1284	-2.4591	9.9858	-0.2264	0.1537	-0.4891	-0.9005	-0.0267	-1.5233	1.1317	1.0342	0.2532	0.5005	0.4097	0.1759	0.4032	0.0373	0.2519	19.7339	-31.013	-1.2764
6	2.815	-2.0444	0.5369	10.785	0.1559	4.208	-0.0781	-0.0162	-0.029	0.0508	-0.0419	0.1468	0.2302	0.4539	0.12	0.3223	0.0853	0.0476	0.3002	0.0391	0.1762	12.3712	-25.1431	4.6254
7	2.3142	-5.4099	-6.3764	15.0411	3.3716	-5.9249	-0.1728	-1.01	0.0952	0.4708	0.3234	0.6701	-0.2182	0.1933	-0.1506	0.7002	0.1823	-0.0576	0.3588	-0.251	0.446	8.9781	-8.3695	8.215
8	5.6086	-1.8727	2.7084	4.8985	4.5706	5.4161	-0.0588	0.4323	0.3104	0.3196	-0.1273	-0.0562	-0.2103	-0.0797	0.1861	0.407	0.0579	0.0354	0.2637	0.0656	0.2103	10.7543	-13.0986	-2.9756
9	1.8668	-5.788	-4.5707	9.624	8.4315	14.1735	0.0243	-0.1115	0.183	-0.0228	0.1544	-0.2148	0.245	0.3547	-0.1787	0.3187	0.0192	-0.0117	0.2813	0.048	0.2255	6.7399	-24.0453	-3.539
10	0.1871	0.0163	-0.1193	1.1436	-0.2735	3.9193	0.0026	0.0917	0.0124	0.2017	0.0646	0.1149	-0.3591	-0.4582	-0.0672	0.2341	0.0126	0	0.2836	0.0269	0.2272	4.8961	-16.463	-6.4948
11	17.581	2.8668	0.9706	6.0997	-3.6567	2.378	-0.3523	0.4653	0.0766	-0.51	0.0231	-0.463	0.0681	0.3299	0.3293	0.22	-0.0049	0.0435	0.3052	0.0089	0.2684	22.206	-18.2866	-23.4437
12	10.7518	17.8686	-3.2039	20.3863	-4.2019	3.5612	-0.4365	-0.1625	-0.1855	-0.4263	-0.2205	-0.5282	0.7235	0.7958	0.657	0.2337	0.2648	0.0411	0.4241	0.0437	0.5604	26.0738	-25.9593	-21.3232
13	13.5399	-2.6266	-9.57	7.5614	-0.5789	6.6687	-0.1988	-0.635	0.0069	0.1865	0.0079	-0.6201	0.1693	0.3954	0.1909	0.2609	0.0033	-0.0581	0.2752	0.0021	0.2425	13.4852	-28.1327	-13.9631
14	3.8067	2.43	-0.4252	3.7932	-2.6037	2.6346	0.0398	-0.088	0.3855	0.0209	0.0805	0.3552	-0.1412	0.071	-0.1203	0.2293	0.0197	0.009	0.3022	-0.0187	0.2416	3.6103	-16.0422	-14.518
15	3.8429	-3.3601	-4.9865	-8.2118	-5.3262	2.5058	-0.4317	0.5711	0.8793	-0.3841	0.1922	-0.7442	0.4275	0.5968	0.2394	0.2219	-0.2706	0.0108	0.6987	0.3671	0.7898	14.964	-5.5605	-22.2175
16	16.5452	6.8146	-11.4668	5.5653	-6.2498	10.0305	0.263	0.4808	-0.0539	0.1738	-0.1657	0.677	-0.5766	0.6826	-0.0973	0.2153	-0.0054	-0.0491	0.3034	-0.0075	0.4163	10.3697	-4.1599	-17.3162
17	29.5862	7.9115	-24.7624	7.7878	5.4258	18.1338	0.8232	0.5252	0.1426	-0.147	-0.2312	0.1472	-1.4559	-0.6455	-0.592	0.3142	0.1983	0.0681	0.231	0.1022	0.6445	2.3226	-3.9282	-10.9934
18	3.4666	-0.2327	0.1352	0.0192	1.6941	4.1718	0.0832	0.3953	0.0947	0.0023	0.0929	-0.0355	-0.1308	-0.0083	-0.1761	0.186	-0.0098	0.0013	0.3226	0.0497	0.2406	-0.2867	-23.7487	-28.9242
19	3.4613	2.9487	1.3948	11.3738	-7.6974	23.3785	0.1457	-0.3519	0.3337	0.2472	0.2287	0.3661	-0.9464	-0.9246	-0.3743	0.2017	0.0379	0.0266	0.3958	-0.0144	0.2726	-7.3542	-19.6555	-30.0783
20	-1.0006	-1.8622	5.0541	7.6831	-2.1847	25.2971	-0.3273	0.11	0.3272	-0.3716	0.1548	0.292	-1.3924	-0.1025	0.1725	0.2859	-0.0209	-0.0507	0.3185	0.0552	0.3518	-6.8978	-17.1704	-37.9348
21	0.1531	0.5038	0.1693	1.72	-0.3205	2.7386	0.0344	0.1866	-0.1039	-0.0925	0.057	0.3829	-0.1197	-0.2128	-0.0914	0.1488	0.0142	-0.0341	0.3972	0.008	0.3432	-6.6563	-30.2575	-34.6481
22	9.2314	1.5423	-1.5249	7.2068	-1.0892	7.4405	0.1193	-0.1014	-0.789	-0.3485	-0.019	0.6833	0.119	-0.9612	-0.1003	0.0406	-0.1439	0.0275	0.4023	-0.0255	0.4646	-12.4158	-43.3814	-26.5895
23	7.1018	-2.9195	-1.7189	5.5918	0.868	1.4949	0.0266	-0.135	-0.3213	0.3954	-0.0083	0.227	0.1288	-0.2717	-0.0183	0.1877	-0.0651	0.0287	0.326	-0.0013	0.3439	-4.5588	-42.8352	-22.7309
24	6.6901	-0.0066	1.7728	3.799	-1.3405	17.2348	0.2642	0.4518	-0.456	-0.1847	-0.1848	-0.1132	0.822	0.033	-0.0793	0.179	-0.0002	0.0117	0.2871	-0.0531	0.2949	0.571	-39.0706	-32.1528
25	6.2725	9.0233	-2.927	26.0285	-7.2077	4.9562	-0.3115	0.5135	-0.5495	-1.2827	-0.0242	-0.462	0.3658	-0.0524	0.3357	0.1558	0.059	-0.0367	0.6258	-0.1078	0.2175	0.4151	-32.1584	-44.4962
26	4.2573	-1.1463	3.9603	2.2483	-1.9163	7.0887	0.0262	0.1916	-0.3786	-0.0317	-0.0024	0.1258	0.1105	-0.0171	-0.0238	0.1646	-0.0256	0.0142	0.3234	-0.0291	0.267	1.8899	-30.3813	-29.061
27	14.6316	-8.3658	-8.8228	4.2965	8.5244	5.0329	-0.2835	1.6642	-1.3301	1.0433	0.3643	0.3138	0.1209	0.6268	-0.0808	0.0481	0.0199	-0.0645	0.6713	-0.1292	0.4068	8.1281	-35.0702	-33.3118
28	2.9661	-0.8409	-0.1077	5.52	5.7005	5.9118	-0.014	0.5232	0.0061	-0.125	0.3611	-0.5558	-0.3054	0.5947	-0.347	0.1631	-0.0342	0.0123	0.4482	0.0466	0.2635	6.1923	-24.8662	-31.6856
29	22.3154	6.9844	0.5255	6.1567	-3.46	4.0061	-0.3731	-0.2583	0.5722	0.5694	0.4337	0.5845	-0.3784	-0.5387	-0.0606	0.2131	0.0829	0.0931	0.3928	0.0257	0.2665	-9.7837	-18.1531	-14.202
30	17.8173	-8.2989	-1.97	10.1491	0.5952	2.2359	-0.4005	-0.6358	-0.7945	0.6416	0.5478	1.3089	0.5243	-0.558	-0.1473	0.2141	-0.0332	0.1353	0.3924	0.116	0.3729	-10.8429	-27.92	-11.5888
31	10.7558	7.4106	-4.007	4.251	-1.9869	4.3799	-0.1997	-0.0965	-0.4745	-0.1355	-0.0323	-0.2615	0.0675	0.2138	0.232	0.2261	0.0103	-0.0122	0.2977	-0.0219	0.304	1.4406	-30.3826	-17.8931
32	5.9248	-1.903	1.7715	4.1501	-1.5823	2.1977	-0.2949	0.1728	0.5507	0.1978	0.2499	0.063	-0.3415	-0.3224	0.045	0.2255	-0.0017	-0.0065	0.3171	0.0292	0.2189	0.376	-15.4585	-24.3877
33	15.6728	-3.8054	3.8882	13.8652	1.8088	13.3418	-0.8752	-0.028	0.922	0.6465	0.3477	0.6024	-0.6658	0.0644	0.5274	0.3083	-0.0017	-0.0392	0.2912	0.0769	0.2999	-3.5228	-9.5811	-28.5131
34	22.5376	-15.9901	-25.1179	37.0351	13.4529	17.9147	0.3422	-0.1881	-0.0726	-1.3785	-0.2384	-0.0411	-0.8479	0.2924	-0.1038	0.308	-0.2489	-0.0777	0.3827	0.1088	0.2152	4.5449	-13.3817	-35.7526

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 20
2	X-RAY DIFFRACTION	2	A	21 - 29
3	X-RAY DIFFRACTION	3	A	30 - 42
4	X-RAY DIFFRACTION	4	A	43 - 54
5	X-RAY DIFFRACTION	5	A	55 - 64
6	X-RAY DIFFRACTION	6	A	65 - 79
7	X-RAY DIFFRACTION	7	A	80 - 86
8	X-RAY DIFFRACTION	8	A	87 - 93
9	X-RAY DIFFRACTION	9	A	94 - 101
10	X-RAY DIFFRACTION	10	A	102 - 119
11	X-RAY DIFFRACTION	11	A	120 - 129
12	X-RAY DIFFRACTION	12	A	130 - 142
13	X-RAY DIFFRACTION	13	A	143 - 155
14	X-RAY DIFFRACTION	14	A	156 - 165
15	X-RAY DIFFRACTION	15	A	166 - 172
16	X-RAY DIFFRACTION	16	A	173 - 178
17	X-RAY DIFFRACTION	17	A	179 - 185
18	X-RAY DIFFRACTION	18	B	8 - 20
19	X-RAY DIFFRACTION	19	B	21 - 26
20	X-RAY DIFFRACTION	20	B	27 - 31
21	X-RAY DIFFRACTION	21	B	32 - 42
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