PDB-2pgf: Crystal structure of adenosine deaminase from Plasmodium vivax in...

ID or keywords:

Entry

Database: PDB / ID: 2pgf

Title

Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine

Components

adenosine deaminase

Keywords

HYDROLASE / Metallo-dependent hydrolase /

Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa Consortium / MSGPP / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI /

Protein Structure Initiative

Function / homology

Function and homology information

S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / 2'-deoxyadenosine deaminase activity /

adenosine deaminase /

adenosine deaminase activity / purine ribonucleoside monophosphate biosynthetic process / purine ribonucleoside salvage /

metal ion binding
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Larson, E.T. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.
Authors: Larson, E.T. / Deng, W. / Krumm, B.E. / Napuli, A. / Mueller, N. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Lauricella, A. / DeTitta, G. / Luft, J. / Zucker, F. / Hol, W.G. / Verlinde, C.L. / Merritt, E.A.

History

Deposition	Apr 9, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 24, 2007	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 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 / struct_conn / struct_conn_type / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Remark 999

SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2pgf.cif.gz	97.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2pgf.ent.gz	74.4 KB	Display	PDB format
PDBx/mmJSON format	2pgf.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/pg/2pgf ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgf	HTTPS FTP

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Related structure data

Related structure data	2pgrC 2qvnC 2amxS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2pgr-d 4o9t-2 4e1y-1 1yfq-d 2d8l-d 2qvn-d 4r27-3 7bop-4 2fa8-d 2yy8-d 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: Pviv005676AAA

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: adenosine deaminase

hetero molecules

43.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	143.962, 146.608, 50.398
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-714- HOH
2	1	A-738- HOH

#1: Protein	adenosine deaminase / Mass: 43477.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: Pv111245 / Plasmid: BG1861 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5KE01, adenosine deaminase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ADN / ADENOSINE / Adenosine Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#4: Chemical	ChemComp-CCN / ACETONITRILE / Acetonitrile Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃N
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.06 Å³/Da / Density % sol: 59.81 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 33% PEG 20000, 0.1 M TAPS (pH 9.0), 0.1 M Sodium phosphate (monobasic), 16% acetonitrile, 5 mM adenosine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97943 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 2007 / Details: mirrors
Radiation	Monochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97943 Å / Relative weight: 1
Reflection	Resolution: 1.89→35 Å / Num. all: 42835 / Num. obs: 42835 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / B_iso Wilson estimate: 24.8 Å² / R_merge(I) obs: 0.073 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.89→1.97 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.473 / Mean I/σ(I) obs: 2.35 / Num. unique all: 4009 / % possible all: 94.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
Blu-Ice		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2AMX

2amx

Resolution: 1.89→35 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.701 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUPS WERE DEFINED USING THE TLSMD SERVER: J.PAINTER & E.A.MERRITT (2006) ACTA CRYST. D62, 439-450, J.PAINTER & E.A.MERRITT (2006) J. ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20061	2144	5 %	RANDOM
R_work	0.15697	-	-	-
all	0.15903	42786	-	-
obs	0.15903	42786	98.36 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 21.575 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.11 Å²	0 Å²	0 Å²
2-	-	-2.13 Å²	0 Å²
3-	-	-	1.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2915	0	26	248	3189

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3095
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2085
X-RAY DIFFRACTION	r_angle_refined_deg	1.058	1.969	4186
X-RAY DIFFRACTION	r_angle_other_deg	0.806	3	5119
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.34	5	378
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.375	25.497	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.491	15	578
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.09	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	457
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3444
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	601
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	704
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	2239
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1581
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	1386
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	225
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.202	0.2	9
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.243	0.2	27
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.871	2.5	2372
X-RAY DIFFRACTION	r_mcbond_other	0.507	2.5	744
X-RAY DIFFRACTION	r_mcangle_it	2.127	3.75	3005
X-RAY DIFFRACTION	r_scbond_it	3.319	4	1422
X-RAY DIFFRACTION	r_scangle_it	4.332	6	1181

LS refinement shell

Resolution: 1.89→1.935 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.226	126	-
R_work	0.219	2537	-
obs	-	2663	83.45 %

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	7.7464	-7.3077	0.5996	7.4027	-1.5608	1.9928	0.3629	0.6174	-0.1151	-0.6089	-0.3704	0.3833	0.0472	-0.0986	0.0075	0.0519	-0.0215	-0.0116	0.1108	-0.0693	0.1216	10.9887	6.0433	18.6956
2	3.5686	0.136	-1.6497	2.9292	-1.2632	6.8905	-0.3919	0.3923	-0.4681	-0.1703	0.0838	0.036	0.1114	-0.6256	0.3082	0.0027	-0.0543	0.0733	0.0987	-0.0845	0.2307	1.388	7.8873	29.575
3	1.3526	0.2367	-0.0018	1.6287	0.058	0.748	-0.0474	0.1098	-0.1708	0.0717	-0.0247	0.1655	-0.0526	-0.0234	0.0721	0.0715	-0.0278	0.0598	0.067	-0.0258	0.1107	16.4636	12.5882	29.792
4	2.7614	0.026	3.159	3.2316	-1.1571	4.6353	0.3097	0.002	-0.3122	0.903	-0.2198	-0.4264	0.5171	0.2872	-0.0899	0.2933	-0.0245	-0.0946	0.0042	0.0342	0.0165	34.1009	5.5502	44.2746
5	2.1055	0.3534	4.0796	14.6478	-1.9912	20.1044	0.2651	-0.5683	-0.1375	1.0455	-0.0524	-0.2358	0.7842	-0.3626	-0.2127	0.4492	-0.1314	-0.0407	0.0184	0.024	-0.1003	29.6825	7.5157	52.969
6	1.3232	-2.1339	0.0165	6.1263	2.0607	1.6227	0.1708	-0.3439	0.0098	0.872	-0.2346	0.156	0.017	-0.0344	0.0638	0.2881	-0.1197	0.0497	0.0831	-0.0245	-0.0139	25.4992	20.5891	47.8381
7	7.8048	-3.2416	-1.7222	6.07	1.1302	3.8352	0.1398	-0.5635	-0.0328	0.5456	0.0419	-0.2442	0.1051	0.2479	-0.1817	0.1936	-0.0802	-0.0613	0.1245	-0.0056	0.0431	36.084	16.5396	44.4689
8	19.2097	7.1386	2.9126	5.1031	1.0148	1.7003	0.1244	-0.1708	-0.5154	0.2982	-0.1001	-0.5214	0.2412	0.223	-0.0243	0.0703	0.0116	-0.0173	0.0684	-0.0012	0.0869	37.7477	6.8667	32.7336
9	1.9434	0.5135	0.6634	1.5386	0.6073	0.8774	0.0329	0.0268	-0.0604	0.1444	0.0007	-0.2562	0.0136	0.1907	-0.0336	0.0618	-0.0358	0.0141	0.0995	0.0023	0.0916	34.9283	13.9598	30.1462
10	3.107	-0.6172	0.1513	12.368	0.8247	2.2901	0.1629	0.1089	-0.0767	-0.4953	-0.0997	-0.1472	0.0426	0.1932	-0.0633	0.0767	-0.0108	0.0483	0.1166	-0.0144	0.0452	28.3012	6.2423	19.1532
11	0.1567	0.6165	0.0326	2.8966	1.5503	4.2934	0.0201	-0.1315	0.0783	0.0897	0.0566	-0.287	-0.139	0.3919	-0.0767	0.0382	-0.0759	-0.0024	0.1479	0.0084	0.0996	39.9955	26.65	31.8072
12	2.0839	0.4405	-0.5624	1.3367	0.2658	1.6718	-0.0299	0.0821	-0.0061	-0.0658	0.0153	-0.132	-0.102	0.2448	0.0146	0.111	-0.062	0.0089	0.1157	0.0186	0.0941	34.3903	26.0794	27.6847
13	2.8109	-0.1002	-1.9264	2.4967	1.4448	6.4694	-0.0942	-0.1716	0.2013	-0.0712	0.0249	-0.0964	-0.6896	0.4935	0.0693	0.1286	-0.1304	-0.0023	0.063	0.0338	0.0573	35.7027	38.1637	27.9307
14	1.2647	0.3933	-0.2342	1.5597	0.3993	1.0744	-0.0168	0.0414	0.2373	-0.0565	-0.0452	0.1597	-0.2545	0.0067	0.062	0.1214	-0.0488	0.0011	0.0379	0.0035	0.1	21.3972	35.4166	30.2415
15	4.8657	1.0265	2.3636	8.9692	1.2752	6.026	0.0659	-0.2056	0.1501	0.7604	-0.3204	0.5204	-0.1153	-0.0797	0.2545	0.1562	-0.0866	0.1104	0.0491	-0.0395	0.0697	17.0685	25.0192	43.5612
16	1.1999	-0.1895	0.5179	2.6094	-0.1755	1.1094	0.0339	-0.0193	0.0784	0.2204	-0.1383	0.3885	-0.0912	-0.0794	0.1045	0.0955	-0.0468	0.0823	0.0826	-0.0337	0.1466	14.2392	23.7436	34.5026
17	7.2936	-2.8984	-0.7235	2.7629	-0.8474	0.8712	-0.0754	-0.1151	-0.0548	0.3478	-0.0033	0.3883	-0.1608	-0.0182	0.0787	0.0502	-0.0435	0.1199	0.0304	-0.0523	0.1583	9.9882	15.9421	35.2723
18	1.6382	0.4279	0.2123	3.0036	0.5347	10.095	0.0719	0.0808	-0.0116	0.1988	-0.0463	0.6307	-0.109	-0.428	-0.0256	0.0156	-0.0202	0.0572	0.0541	-0.04	0.219	4.793	19.8264	28.7597
19	7.8698	1.9191	-1.1902	4.4469	-0.54	2.3643	-0.0849	0.3009	-0.0314	-0.3403	-0.0573	0.1812	-0.134	-0.0816	0.1422	0.0981	-0.0172	-0.0049	0.0948	0.0001	0.0617	18.043	22.3983	19.2053
20	12.2982	7.5971	-0.7891	8.3085	-1.3224	6.8348	-0.3998	0.5833	-0.086	-0.6814	0.1022	0.0515	0.1323	-0.0845	0.2975	0.1	-0.0322	0.0099	0.1184	-0.0344	-0.0006	18.6406	15.4947	12.0869

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	5 - 14	13 - 22
2	X-RAY DIFFRACTION	2	A	A	15 - 28	23 - 36
3	X-RAY DIFFRACTION	3	A	A	29 - 47	37 - 55
4	X-RAY DIFFRACTION	4	A	A	48 - 65	56 - 73
5	X-RAY DIFFRACTION	5	A	A	66 - 75	74 - 83
6	X-RAY DIFFRACTION	6	A	A	76 - 88	84 - 96
7	X-RAY DIFFRACTION	7	A	A	89 - 100	97 - 108
8	X-RAY DIFFRACTION	8	A	A	101 - 111	109 - 119
9	X-RAY DIFFRACTION	9	A	A	112 - 153	120 - 161
10	X-RAY DIFFRACTION	10	A	A	154 - 166	162 - 174
11	X-RAY DIFFRACTION	11	A	A	167 - 189	175 - 197
12	X-RAY DIFFRACTION	12	A	A	190 - 203	198 - 211
13	X-RAY DIFFRACTION	13	A	A	204 - 218	212 - 226
14	X-RAY DIFFRACTION	14	A	A	219 - 278	227 - 286
15	X-RAY DIFFRACTION	15	A	A	279 - 288	287 - 296
16	X-RAY DIFFRACTION	16	A	A	289 - 318	297 - 326
17	X-RAY DIFFRACTION	17	A	A	319 - 329	327 - 337
18	X-RAY DIFFRACTION	18	A	A	330 - 337	338 - 345
19	X-RAY DIFFRACTION	19	A	A	338 - 351	346 - 359
20	X-RAY DIFFRACTION	20	A	A	352 - 363	360 - 371

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