PDB-4x45: Crystal Structure of F173G Mutant of Human APRT

ID or keywords:

Entry

Database: PDB / ID: 4x45

Title

Crystal Structure of F173G Mutant of Human APRT

Components

Adenine phosphoribosyltransferase

Keywords

TRANSFERASE / APRT

Function / homology

Function and homology information

Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / Purine salvage / GMP salvage / IMP salvage / AMP salvage ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.75 Å

Authors

Pereira, H.M. / Pimenta, A. / Mercaldi, G. / Thiemann, O.H.

Citation

Journal: To Be Published
Title: Crystal Structure of F173G Mutant of Human APRT
Authors: Pimenta, A. / Pereira, H.M. / Merdaldi, G. / Thiemann, O.H.

History

Deposition	Dec 2, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x45.cif.gz	157 KB	Display	PDBx/mmCIF format
PDB format	pdb4x45.ent.gz	122.9 KB	Display	PDB format
PDBx/mmJSON format	4x45.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x45_validation.pdf.gz	783.8 KB	Display	wwPDB validaton report
Full document	4x45_full_validation.pdf.gz	786.7 KB	Display
Data in XML	4x45_validation.xml.gz	19 KB	Display
Data in CIF	4x45_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/4x45 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/4x45	HTTPS FTP

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Related structure data

Related structure data	4x44
Similar structure data	6fci-1 1zn9-d 6hgq-1 6fd4-d 1zn7-d 6hgq-2 6hgs-d 6fch-d 4okm-3 1l1r-1 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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (5) #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: Adenine phosphoribosyltransferase

B: Adenine phosphoribosyltransferase

hetero molecules

39.4 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)	47.748, 140.617, 49.216
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Adenine phosphoribosyltransferase / APRT Mass: 19539.604 Da / Num. of mol.: 2 / Mutation: F173G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APRT / Plasmid: pet29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P07741, adenine phosphoribosyltransferase
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.13 Å³/Da / Density % sol: 42.21 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22,5% PEG 4000, 85mM Tris pH8.5, 170mM Sodium Acetate, 15% Glycerol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: D03B-MX1 / Wavelength: 1.458 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 8, 2008

Radiation

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

Radiation wavelength

Wavelength: 1.458 Å / Relative weight: 1

Reflection

Resolution: 1.75→70.36 Å / Num. all: 34302 / Num. obs: 34302 / % possible obs: 98 % / Redundancy: 3.6 % / R_merge(I) obs: 0.08 / R_pim(I) all: 0.047 / R_rim(I) all: 0.093 / R_sym value: 0.08 / Net I/av σ(I): 5.393 / Net I/σ(I): 11.2 / Num. measured all: 124507

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.75-1.84	3.3	0.483	1.4	16023	4860	0.296	0.483	2.5	96.9
1.84-1.96	3.7	0.303	2.2	16953	4624	0.174	0.303	4.3	97.4
1.96-2.09	3.7	0.194	3.4	15956	4371	0.111	0.194	6.7	96.9
2.09-2.26	3.6	0.137	4.6	14647	4057	0.079	0.137	9.4	97.2
2.26-2.47	3.6	0.105	3.1	13739	3812	0.063	0.105	11.8	98.4
2.47-2.77	3.7	0.081	7.3	12817	3503	0.048	0.081	13.9	99.3
2.77-3.2	3.7	0.081	6.9	11556	3106	0.047	0.081	17	99.5
3.2-3.91	3.8	0.066	8.3	10249	2669	0.038	0.066	21.6	99.7
3.91-5.53	3.9	0.05	10.2	8194	2102	0.029	0.05	25	99.1
5.53-142.857	3.7	0.047	12.4	4373	1198	0.028	0.047	24.2	96.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.25	data scaling
MOLREP		phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→46.453 Å / FOM work R set: 0.8734 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1993	1679	5.01 %	Random selection
R_work	0.1798	31833	-	-
obs	0.1809	33512	97.69 %	-

Solvent computation

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

Displacement parameters

B_iso max: 68.38 Å² / B_iso mean: 24.27 Å² / B_iso min: 9.13 Å²

Refinement step

Cycle: final / Resolution: 1.75→46.453 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2691	0	23	373	3087
B_iso mean	-	-	31.02	34.94	-
Num. residues	-	-	-	-	354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2767
X-RAY DIFFRACTION	f_angle_d	0.887	3753
X-RAY DIFFRACTION	f_chiral_restr	0.059	430
X-RAY DIFFRACTION	f_plane_restr	0.004	485
X-RAY DIFFRACTION	f_dihedral_angle_d	14	1050

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 (%)
1.75-1.8015	0.2934	138	0.2795	2573	X-RAY DIFFRACTION	97
1.8015-1.8597	0.2515	126	0.2373	2603	X-RAY DIFFRACTION	97
1.8597-1.9261	0.227	127	0.2104	2604	X-RAY DIFFRACTION	97
1.9261-2.0033	0.2349	123	0.2027	2591	X-RAY DIFFRACTION	96
2.0033-2.0944	0.2356	146	0.1956	2599	X-RAY DIFFRACTION	97
2.0944-2.2049	0.2277	127	0.186	2614	X-RAY DIFFRACTION	97
2.2049-2.343	0.1856	162	0.1806	2605	X-RAY DIFFRACTION	97
2.343-2.5239	0.194	121	0.1734	2678	X-RAY DIFFRACTION	98
2.5239-2.7779	0.1872	156	0.1857	2674	X-RAY DIFFRACTION	99
2.7779-3.1797	0.2254	151	0.1805	2721	X-RAY DIFFRACTION	99
3.1797-4.0058	0.1958	146	0.1573	2749	X-RAY DIFFRACTION	99
4.0058-46.47	0.1629	156	0.1594	2822	X-RAY DIFFRACTION	97

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	3.1597	0.2025	-1.1208	5.436	2.4221	7.2352	-0.2883	-0.3294	-0.69	0.6178	0.0801	-0.194	1.6502	0.1536	0.1418	0.367	0.0063	0.0086	0.2627	0.0311	0.2958	-3.3991	-5.7378	20.808
2	3.8129	-0.9813	-1.2015	0.3067	0.191	0.5128	-0.1968	0.0514	0.1178	0.1552	0.1068	0.0298	0.0097	0.009	0.0974	0.1338	0.0087	0.0079	0.1752	0.012	0.1649	-11.0796	5.8603	28.8058
3	0.7107	0.282	0.5938	0.6223	-0.2406	3.9542	-0.0244	0.0162	-0.1516	-0.0691	0.0402	-0.0793	0.2171	0.1591	-0.0195	0.121	-0.0105	0.0124	0.1138	-0.0099	0.1094	-0.5273	1.9378	10.3741
4	1.5329	0.1438	0.3237	1.5833	-0.3218	2.3332	0.0303	-0.0682	0.1219	0.0577	-0.0152	0.0267	-0.0786	0.118	-0.0304	0.1148	-0.0127	-0.0059	0.1291	-0.005	0.1566	-0.6805	12.5643	10.1619
5	1.3115	-0.8024	-0.7338	1.9984	0.5588	0.5097	-0.1629	-0.1977	0.0744	0.2499	0.0339	0.1148	-0.0916	0.0259	0.111	0.202	0.0159	-0.0478	0.1634	-0.0475	0.1803	-3.0817	24.6398	12.7834
6	3.8027	1.9731	-2.589	1.509	-1.3218	3.0707	0.1467	-0.3472	0.6649	0.1954	0.1524	0.8148	-0.0061	-0.2301	-0.136	0.2795	0.0389	-0.009	0.2419	-0.055	0.429	-14.762	25.9652	15.7364
7	0.255	0.0556	0.141	1.6526	0.7752	0.5463	-0.0462	-0.0461	0.1823	-0.2874	0.0395	0.3251	-0.2922	-0.0184	0.0021	0.1659	0.0147	-0.0495	0.1515	-0.0019	0.1795	-7.0781	17.514	6.7679
8	0.5721	-0.0411	-0.3718	2.0385	-0.2005	1.5608	-0.1286	-0.0148	0.1458	-0.19	0.0261	0.5148	-0.2276	-0.1179	0.0478	0.1843	0.0247	-0.0907	0.1836	-0.0161	0.2677	-11.5171	18.1193	5.2586
9	0.5803	-0.2142	0.6817	1.2563	-0.6572	1.4392	-0.0651	0.6919	0.4317	-0.2108	0.0167	0.1312	0.0882	-0.1652	-0.0425	0.1256	0.0111	-0.0006	0.3046	0.055	0.1961	-19.3177	7.5613	13.8195
10	0.8521	-0.3509	-0.5428	1.4748	1.1842	2.2576	-0.4301	0.5379	0.3926	-0.1983	0.3177	0.4286	0.1264	-0.4471	-0.2613	0.1041	-0.041	-0.0491	0.3024	0.1099	0.2151	-14.8367	4.2116	12.0786
11	9.26	0.4792	-0.5826	5.7177	1.8091	8.2715	-0.0761	0.4411	0.369	-0.0455	-0.2776	-0.7329	0.5206	0.4815	0.3369	0.2219	0.0383	-0.0213	0.2395	0.0298	0.2327	19.4503	22.345	10.505
12	0.4161	-0.997	-0.4687	2.6952	0.7455	1.3133	-0.0623	-0.1406	0.5031	-0.1524	-0.0706	-0.2348	-0.3717	-0.0236	0.1644	0.2308	0.0147	-0.0766	0.2005	-0.07	0.3422	5.8592	31.2875	13.7318
13	1.74	-0.6074	1.6965	0.7043	-1.2998	2.593	-0.0438	0.0537	0.0033	-0.026	0.0093	-0.0301	0.0996	0.0869	-0.0034	0.1406	0.0186	0.0251	0.1599	-0.0098	0.1765	16.703	14.3361	17.6539
14	1.9294	-0.2023	0.0277	1.4901	-0.867	2.3286	-0.0336	0.0249	0.0855	-0.009	0.1141	-0.0186	0.0451	-0.2294	-0.102	0.178	-0.0346	-0.0136	0.1996	-0.0221	0.1656	8.1139	12.3388	23.988
15	2.3946	-0.8255	-0.9146	1.0024	0.9007	1.4234	0.0706	0.1198	0.0698	-0.0846	-0.157	0.0262	-0.3302	-0.1691	0.0849	0.2293	-0.0036	-0.0233	0.2005	-0.0039	0.1447	-2.7247	13.3893	30.2926
16	1.1893	-0.0958	-0.4084	3.6538	0.743	0.5542	-0.0236	0.1146	0.2327	-0.2331	0.0554	0.0005	-0.4964	-0.1581	0.0442	0.3669	0.0236	-0.0614	0.1561	0.0049	0.1783	-3.0973	20.8347	37.1424
17	1.728	0.6037	-0.4361	0.3425	0.2536	1.1934	0.0141	-0.221	-0.0392	0.0707	0.0083	0.1832	0.0459	0.0937	-0.0217	0.172	0.033	0.0165	0.1571	0.0026	0.1506	7.4894	14.6379	32.2378
18	1.6662	0.5089	-0.26	4.2898	-2.0331	1.8846	-0.1399	-0.0309	0.0176	0.35	0.0352	-0.119	-0.1921	-0.0543	0.0932	0.2061	0.0453	0.0592	0.2032	-0.0043	0.1783	5.4874	19.1373	37.2884
19	1.0762	-0.2103	-0.0296	1.6659	-0.5243	0.9358	0.1018	-0.2114	0.2246	0.4163	-0.0223	-0.0067	-0.4233	0.1807	-0.076	0.2448	-0.0161	0.0083	0.162	-0.031	0.1646	13.8122	24.0738	30.9783
20	1.7675	-0.04	0.1399	2.1305	0.1084	2.906	0.1452	0.0489	0.2634	0.1685	-0.2025	-0.1984	-0.7226	0.462	0.0479	0.23	-0.0245	-0.0052	0.1746	-0.0147	0.2352	16.9219	26.2131	25.6288

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 12 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 35 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 54 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 55 through 79 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 95 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 96 through 113 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 114 through 133 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 134 through 155 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 156 through 168 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 169 through 180 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2 through 10 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 11 through 35 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 36 through 54 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 55 through 79 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 80 through 95 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 96 through 113 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 114 through 133 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 134 through 146 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 147 through 168 )	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 169 through 180 )	B

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