PDB-5kam: Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase ...

ID or keywords:

Entry

Database: PDB / ID: 5kam

Title

Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with Inosine 5' monophosphate

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE / inhibitor / complex / dimer / enzyme

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage ...
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.481 Å

Authors

Teran, D. / Guddat, L.

Citation

Journal: Sci Rep / Year: 2016
Title: Crystal structures and inhibition of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltransferase.
Authors: Teran, D. / Hockova, D. / Cesnek, M. / Zikova, A. / Naesens, L. / Keough, D.T. / Guddat, L.W.

History

Deposition	Jun 1, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kam.cif.gz	154.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5kam.ent.gz	120.7 KB	Display	PDB format
PDBx/mmJSON format	5kam.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kam_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5kam_full_validation.pdf.gz	1 MB	Display
Data in XML	5kam_validation.xml.gz	14.9 KB	Display
Data in CIF	5kam_validation.cif.gz	19.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ka/5kam ftp://data.pdbj.org/pub/pdb/validation_reports/ka/5kam	HTTPS FTP

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Related structure data

Related structure data	5jsqSC 5jv5C 5k51C 5kapC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5kap-1 5kap-2 4pjv-1 5k51-2 4naj-d 3khn-d 2gcd-2 6kkk-1 2vuu-6 2rfc-3 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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (6)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

A: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

defined by author&software
49.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

C: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

defined by author&software
49.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.054, 109.819, 45.292
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	17
Space group name H-M	P22₁2

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase Mass: 24221.775 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli) References: UniProt: Q07010, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-IMP / INOSINIC ACID Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.41 Å³/Da / Density % sol: 49.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris PH range: 5-5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 2.48→43.23 Å / Num. obs: 17272 / % possible obs: 99.8 % / Redundancy: 7.2 % / R_merge(I) obs: 0.079 / Net I/σ(I): 14
Reflection shell	Resolution: 2.48→2.58 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PHASES		phasing
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq

Resolution: 2.481→43.23 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.3

	R_factor	Num. reflection	% reflection
R_free	0.2849	1717	9.98 %
R_work	0.2522	-	-
obs	0.2555	17201	99.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.481→43.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2592	0	71	38	2701

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	2717
X-RAY DIFFRACTION	f_angle_d	0.474	3705
X-RAY DIFFRACTION	f_dihedral_angle_d	14.737	1632
X-RAY DIFFRACTION	f_chiral_restr	0.043	441
X-RAY DIFFRACTION	f_plane_restr	0.003	459

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 (%)
2.4809-2.5539	0.4272	138	0.3287	1239	X-RAY DIFFRACTION	98
2.5539-2.6363	0.3349	139	0.3249	1254	X-RAY DIFFRACTION	99
2.6363-2.7305	0.376	140	0.3139	1263	X-RAY DIFFRACTION	100
2.7305-2.8398	0.3417	142	0.3014	1291	X-RAY DIFFRACTION	100
2.8398-2.969	0.2984	141	0.275	1267	X-RAY DIFFRACTION	100
2.969-3.1255	0.2964	140	0.2785	1262	X-RAY DIFFRACTION	100
3.1255-3.3213	0.297	141	0.252	1289	X-RAY DIFFRACTION	100
3.3213-3.5776	0.3305	144	0.2751	1282	X-RAY DIFFRACTION	100
3.5776-3.9374	0.3054	142	0.2476	1292	X-RAY DIFFRACTION	100
3.9374-4.5067	0.2633	147	0.2034	1320	X-RAY DIFFRACTION	100
4.5067-5.6759	0.2078	147	0.2126	1325	X-RAY DIFFRACTION	100
5.6759-43.2366	0.258	156	0.2536	1400	X-RAY DIFFRACTION	99

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	6.5043	-1.0845	1.8214	5.6935	-1.8905	3.221	0.6328	-2.1737	2.1386	0.683	-0.3497	0.4467	-0.5713	-0.2892	-0.0687	0.7227	-0.2996	0.2675	0.8217	-0.276	1.2806	7.0573	121.5406	57.1297
2	7.1646	3.6113	2.8696	3.5319	3.8651	4.8665	1.0245	0.108	1.3062	1.1432	-0.3383	-0.0464	0.8875	-0.1308	-0.4566	0.5128	0.0684	0.0918	0.4362	0.0537	0.4478	3.5855	114.4457	49.2254
3	2.4613	-0.8511	-1.3962	4.0443	3.3425	2.0171	1.064	-0.2528	2.6358	0.202	-0.1248	0.4072	-0.2728	0.1251	-0.5287	0.5092	-0.0216	0.3302	0.6546	-0.1606	1.45	0.1478	121.2783	50.9845
4	1.68	-1.8441	2.3371	3.0142	-1.7553	4.2874	0.8907	1.2091	1.8005	0.2936	0.0032	0.6515	-0.1656	-0.4461	-0.3737	0.3812	0.0814	0.2017	0.6353	0.4102	1.1251	9.9413	118.9745	43.2868
5	0.842	-0.8621	2.5122	7.376	-1.487	7.7711	0.3042	1.6367	2.2159	-1.0565	0.4472	0.3876	-0.1531	0.3144	-0.2824	0.531	-0.0545	0.1651	0.9899	0.5055	1.193	11.8304	123.0183	39.1566
6	6.8537	-2.6709	-2.6808	4.8754	-0.2216	4.5139	1.1526	0.5685	2.2099	-0.2864	-0.0877	-0.3186	-0.1821	0.1352	-0.7175	0.3778	-0.0354	0.041	0.5451	0.1424	0.805	20.3356	117.0276	47.6034
7	3.7821	3.8995	-1.8012	4.3055	-1.7379	0.8917	0.6005	-1.0069	-2.7213	-0.1014	-0.8128	-0.5218	0.4121	0.1744	0.001	0.5073	-0.0412	-0.1799	0.4269	0.0924	1.1468	14.795	103.5731	50.7979
8	1.2705	0.2873	2.5553	0.1973	0.5178	5.1253	0.3883	-0.6846	-0.8503	0.8867	-0.2202	-1.2441	0.5596	0.4027	0.0813	0.4598	-0.0395	-0.4183	0.7048	0.4877	1.2564	10.436	101.6165	55.8087
9	1.1225	-0.5714	-0.6743	0.5515	0.1035	0.6312	0.1482	0.4051	-0.1721	0.0224	-0.0584	-0.1247	0.0628	0.2266	0.0301	0.4901	0.286	-0.2081	1.7994	0.6436	2.4166	19.7207	91.6889	51.2345
10	4.7847	-0.7006	0.9986	3.6039	-0.7779	0.8448	0.417	-0.4188	0.0344	0.5046	-0.3034	-0.3012	0.0094	-0.0156	-0.0711	0.3793	-0.1524	-0.016	0.3636	-0.0439	0.2539	-40.6971	62.0624	74.4221
11	2.2241	1.3595	1.6638	3.5526	4.5267	5.7212	-0.162	0.0829	1.0032	0.2106	-0.1681	0.6734	0.2052	0.3229	0.4175	0.2881	-0.0754	0.0451	0.2827	-0.0281	0.3845	-47.0103	66.3454	67.3076
12	2.9934	-1.3929	1.9832	8.3256	-2.6294	2.8852	0.0756	0.7097	0.223	0.2049	-0.1796	-0.5952	0.0863	0.4171	0.131	0.2832	0.0224	0.1404	0.396	0.1301	0.1556	-37.522	64.4333	62.2022
13	3.838	-1.0996	0.104	6.8344	0.4177	3.6305	0.2082	0.57	-0.0122	-0.3819	0.373	-0.3084	-0.3139	0.3793	-0.4179	0.3193	-0.1185	0.0708	0.4948	0.0888	0.3012	-33.3752	65.5985	60.5221
14	9.6581	-0.7338	-6.8108	4.5599	3.2307	9.5205	0.3193	0.4149	0.4634	-0.0224	0.7393	-0.5545	0.1443	-0.0424	-1.1942	0.32	-0.0678	-0.0753	0.724	-0.0241	0.4987	-26.7648	64.6085	65.2527
15	8.3885	3.8521	2.0901	9.1071	1.9708	2.8865	-0.0951	0.1928	-1.2298	-0.3044	0.5397	-1.309	0.1527	0.3561	-0.4148	0.3141	-0.0231	-0.0041	0.3718	-0.0425	0.4182	-32.275	48.5621	70.1895
16	1.2031	3.1167	-0.1081	8.1289	-0.8625	3.947	0.6116	0.0829	-0.9874	0.5177	-0.5596	-2.0796	0.4037	-0.0494	-0.017	0.3594	-0.0393	-0.1814	0.3956	0.1576	0.5526	-35.4381	45.4353	74.9238
17	4.3371	-4.1748	1.7075	4.5952	-0.0103	5.358	0.6388	0.7624	0.6409	0.2288	-0.0074	-1.4804	0.6842	1.4936	-0.4238	0.4561	0.401	-0.0992	0.5146	0.0452	1.7347	-29.6057	33.664	65.5794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 65 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 79 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 80 through 119 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 120 through 141 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 142 through 158 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 159 through 178 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 179 through 187 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 188 through 192 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 5 through 69 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 70 through 79 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 80 through 119 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 120 through 148 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 149 through 158 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 159 through 178 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 179 through 188 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 189 through 199 )

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