PDB-6aps: Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase...

ID or keywords:

Entry

Database: PDB / ID: 6aps

Title

Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with [(2-((Guanine-9H-yl)methyl)propane-1,3 diyl)bis(oxy)]bis(methylene))diphosphonic acid

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE / Trypanosoma brucei / Purine salvage / acyclic nucleoside biphosphonate

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 / nuclear lumen ...
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.762 Å

Authors

Teran, D. / Guddat, L.W.

Citation

Journal: PLoS Negl Trop Dis / Year: 2018
Title: Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery.
Authors: Dolezelova, E. / Teran, D. / Gahura, O. / Kotrbova, Z. / Prochazkova, M. / Keough, D. / Spacek, P. / Hockova, D. / Guddat, L. / Zikova, A.

History

Deposition	Aug 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

-
Download

PDBx/mmCIF format	6aps.cif.gz	172.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6aps.ent.gz	135.9 KB	Display	PDB format
PDBx/mmJSON format	6aps.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6aps_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6aps_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6aps_validation.xml.gz	21.8 KB	Display
Data in CIF	6aps_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/6aps ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6aps	HTTPS FTP

-
Related structure data

Related structure data	6aptC 6apuC 6apvC 6aqoC 6ar9C 5jsqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jv5-d 6uwl-d 6h18-d 4tvj-1 4m4s-d 2ise-2 3vrm-d 2ffk-d 6h6k-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

-
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

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	116.013, 93.885, 44.715
Angle α, β, γ (deg.)	90.00, 107.80, 90.00
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 2 molecules AB

#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

-
Non-polymers , 6 types, 380 molecules

#2: Chemical	ChemComp-SV2 / [{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid) Mass: 427.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₉N₅O₉P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.6 %
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: 5-7

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 10, 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: 1.76→46.94 Å / Num. obs: 44556 / % possible obs: 98.9 % / Redundancy: 3.7 % / R_pim(I) all: 0.087 / Net I/σ(I): 8.2
Reflection shell	Resolution: 1.76→1.8 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2210 / R_pim(I) all: 0.561 / % possible all: 85.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq

Resolution: 1.762→42.575 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1921	2000	4.49 %
R_work	0.158	-	-
obs	0.1595	44540	98.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.762→42.575 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2886	0	91	371	3348

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	3116
X-RAY DIFFRACTION	f_angle_d	1.561	4241
X-RAY DIFFRACTION	f_dihedral_angle_d	10.787	2557
X-RAY DIFFRACTION	f_chiral_restr	0.103	482
X-RAY DIFFRACTION	f_plane_restr	0.01	532

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 (%)
1.7615-1.8056	0.3954	117	0.3424	2715	X-RAY DIFFRACTION	88
1.8056-1.8544	0.2648	160	0.2623	3057	X-RAY DIFFRACTION	100
1.8544-1.909	0.2629	142	0.2046	3032	X-RAY DIFFRACTION	100
1.909-1.9706	0.2559	129	0.1767	3064	X-RAY DIFFRACTION	100
1.9706-2.041	0.1808	151	0.1667	3085	X-RAY DIFFRACTION	100
2.041-2.1227	0.2201	148	0.1644	3064	X-RAY DIFFRACTION	100
2.1227-2.2193	0.2009	136	0.1535	3041	X-RAY DIFFRACTION	100
2.2193-2.3363	0.1673	152	0.1462	3067	X-RAY DIFFRACTION	100
2.3363-2.4827	0.1987	140	0.1464	3094	X-RAY DIFFRACTION	100
2.4827-2.6744	0.2022	146	0.1491	3048	X-RAY DIFFRACTION	100
2.6744-2.9434	0.1784	144	0.1566	3059	X-RAY DIFFRACTION	100
2.9434-3.3692	0.1733	148	0.1405	3067	X-RAY DIFFRACTION	100
3.3692-4.2442	0.1637	144	0.1295	3071	X-RAY DIFFRACTION	99
4.2442-42.5871	0.1668	143	0.1534	3076	X-RAY DIFFRACTION	98

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	8.2147	1.5992	2.9108	6.5398	-1.9283	7.4082	0.1316	-0.4172	-0.2641	-0.0935	0.2393	1.2399	0.106	-0.6139	-0.3073	0.185	-0.0141	0.0364	0.1746	0.0739	0.3288	113.5347	-38.1712	62.7914
2	4.2257	0.8341	0.0795	2.187	-0.488	0.7848	0.1025	-0.2693	-0.0495	0.298	-0.0691	-0.2451	0.0085	0.0947	-0.0355	0.1576	0.0261	-0.0281	0.1107	-0.0328	0.0911	139.7577	-27.492	64.4428
3	4.1755	0.3455	1.354	2.9106	0.834	3.1532	-0.0311	0.0393	-0.0144	0.0591	0.093	-0.1486	-0.0498	0.04	-0.0604	0.1197	0.0152	0.0026	0.0979	0.0057	0.0503	133.7597	-24.4917	59.5594
4	6.3949	1.3064	0.9	3.305	1.2688	1.3627	-0.1485	0.361	0.6315	-0.3021	0.1492	-0.0711	-0.0517	0.149	0.017	0.1461	-0.0105	0.0278	0.1783	0.0136	0.1141	139.4865	-30.5681	52.0898
5	7.4148	6.3509	1.5357	8.328	1.1284	1.266	-0.3426	0.6889	-0.4715	-0.5305	0.4465	-0.8872	0.0601	0.4488	-0.154	0.2523	-0.0082	0.0938	0.2283	-0.0775	0.2138	142.3995	-35.9235	46.6701
6	2.5417	-0.8833	0.0007	2.1775	0.1115	0.5114	-0.0372	0.0827	-0.131	-0.0663	0.0736	0.0702	0.0813	0.0448	-0.0302	0.1506	-0.0052	0.0071	0.1236	-0.0088	0.0483	127.8501	-37.9398	56.0197
7	7.2124	2.0782	-2.6477	6.7861	-2.2939	2.0094	0.0867	0.4761	-1.2096	-0.6329	0.0903	0.1011	1.4413	-1.0226	-0.1505	0.4489	-0.0824	-0.1162	0.3626	-0.1307	0.6012	109.208	-41.2411	45.6742
8	2.5621	-1.8041	-3.122	6.1544	1.6821	3.9251	-0.4515	-0.8478	0.4649	0.6948	0.4899	-1.1218	0.1207	0.3084	-0.0383	0.2668	0.0541	-0.0985	0.2445	-0.0791	0.2539	133.8592	-7.5471	70.034
9	3.276	-0.0183	1.1389	2.416	0.7489	2.6947	0.0318	-0.1288	-0.0082	0.0523	-0.0674	0.4515	0.002	-0.3149	0.0239	0.1088	0.0062	0.0244	0.1186	0.0415	0.1498	112.0237	-17.9701	55.8915
10	5.2582	0.8642	-0.3254	3.1329	-0.4956	2.3439	-0.0881	0.0553	-0.0842	-0.1482	0.1104	0.1734	0.0388	-0.0053	-0.027	0.109	0.0148	0.0064	0.1065	0.0171	0.0578	119.2828	-21.4977	54.4684
11	4.8046	1.8747	5.3689	7.7342	1.2761	7.7371	0.5096	1.2955	-0.7681	-0.6535	-0.1043	-0.3586	0.6676	0.7245	-0.5135	0.318	0.0617	-0.0565	0.3422	0.0072	0.2016	113.295	-21.0434	38.6878
12	0.328	0.4734	0.1292	2.963	-0.1584	0.767	0.012	0.073	0.0555	-0.1122	-0.0004	-0.0165	-0.1767	0.0563	-0.0049	0.1496	-0.0087	0.0175	0.1782	0.0162	0.0675	120.8819	-10.391	49.7106
13	6.4013	5.6226	5.7007	7.1041	6.9262	6.8492	-0.4668	0.5806	0.2949	-0.7838	0.2158	0.356	-0.5124	-0.0994	0.2138	0.2573	-0.0337	-0.0318	0.2244	0.0576	0.0925	119.7457	-9.6354	39.5588
14	6.7454	2.669	4.9689	4.389	2.7655	5.6839	-0.0863	-0.032	0.2288	-0.1804	-0.0063	0.3541	-0.2526	-0.2643	0.1087	0.1124	0.0242	0.0031	0.1616	0.0248	0.0814	116.8107	-8.773	49.4075
15	2.6769	0.4082	1.5437	1.1908	0.1898	1.1061	-0.0091	0.0469	0.2021	-0.0525	0.0192	0.0833	-0.1196	0.0109	-0.0061	0.1646	0.0081	0.0368	0.1192	0.0212	0.0996	122.9395	-2.7542	54.494
16	3.83	-0.1177	-0.7738	1.6791	0.4196	4.3864	-0.0143	0.0118	0.6103	0.1724	0.0708	-0.4692	-0.3377	0.2795	-0.044	0.1463	-0.0152	-0.0299	0.1193	0.0037	0.2444	138.5675	-9.969	61.1398

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 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 132 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 133 through 188 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 189 through 199 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 16 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 17 through 53 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 54 through 79 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 80 through 107 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 108 through 119 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 120 through 132 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 133 through 148 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 149 through 168 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 169 through 196 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 380 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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

-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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 380 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-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

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 380 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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