PDB-6d9q: The sulfate-bound crystal structure of HPRT (hypoxanthine phospho...

ID or keywords:

Entry

Database: PDB / ID: 6d9q

Title

The sulfate-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)

Components

Hypoxanthine phosphoribosyltransferase

Keywords

TRANSFERASE / HPRT / hypoxanthine phosphoribosyltransferase

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding ...
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.056 Å

Authors

Satyshur, K.A. / Dubiel, K. / Anderson, B. / Wolak, C. / Keck, J.L.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM084003	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM07215	United States
National Science Foundation (NSF, United States)	DGE-1256259	United States

Citation

Journal: Elife / Year: 2019
Title: Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction.
Authors: Anderson, B.W. / Liu, K. / Wolak, C. / Dubiel, K. / She, F. / Satyshur, K.A. / Keck, J.L. / Wang, J.D.

History

Deposition	Apr 30, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6d9q.cif.gz	430.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6d9q.ent.gz	363.4 KB	Display	PDB format
PDBx/mmJSON format	6d9q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6d9q_validation.pdf.gz	471.3 KB	Display	wwPDB validaton report
Full document	6d9q_full_validation.pdf.gz	475.9 KB	Display
Data in XML	6d9q_validation.xml.gz	31.2 KB	Display
Data in CIF	6d9q_validation.cif.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9q ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9q	HTTPS FTP

-
Related structure data

Related structure data	6d9rC 6d9sC 3h83S 3kb8 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4rqa-2 4rqb-3 4lao-d 4z1o-1 1r3u-1 3mz4-d 6omp-d 4zfn-1 4lan-d 3ohp-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (5)

Deposited unit

A: Hypoxanthine phosphoribosyltransferase

B: Hypoxanthine phosphoribosyltransferase

C: Hypoxanthine phosphoribosyltransferase

D: Hypoxanthine phosphoribosyltransferase

hetero molecules

82.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, By Gel filtration, apo and inhibitor bound are sequestered as tetramers, but the substrate is native dimer.

Unit cell

Length a, b, c (Å)	82.597, 82.597, 242.416
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Hypoxanthine phosphoribosyltransferase / HPRT Mass: 20503.646 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) Gene: hpt, hprT, hpt1, tilS, BA_0063, A9486_05730, ABW01_27435, BASH2_00187, BVG01_28865, CN272_24955, CN488_12230, CN504_22375, COE56_22980, COJ30_24475, COK92_19380, COL95_25280, MCCC1A01412_27610 Plasmid: pLIC-trPC-HA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A1S0QLD4, UniProt: B9ZW32*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.91 Å³/Da / Density % sol: 57.74 % / Description: Long rhomboidal crystals
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.01 M cobalt [II] chloride hexahydrate, 0.1 M MES monohydrate, pH 6.5, 1.8 M ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2015
Radiation	Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.056→50 Å / Num. obs: 60325 / % possible obs: 99.2 % / Redundancy: 10.8 % / R_pim(I) all: 0.037 / R_rim(I) all: 0.124 / Net I/σ(I): 24.8
Reflection shell	Resolution: 2.056→2.13 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 5683 / CC_1/2: 0.804 / R_rim(I) all: 0.888 / Χ²: 0.848 / % possible all: 94.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
ADSC		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3H83

3h83

Resolution: 2.056→41.299 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.29

	R_factor	Num. reflection	% reflection
R_free	0.2166	1983	3.29 %
R_work	0.1827	-	-
obs	0.1838	60189	99.12 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.056→41.299 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5686	0	46	440	6172

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5883
X-RAY DIFFRACTION	f_angle_d	0.569	7970
X-RAY DIFFRACTION	f_dihedral_angle_d	9.886	3574
X-RAY DIFFRACTION	f_chiral_restr	0.048	938
X-RAY DIFFRACTION	f_plane_restr	0.003	992

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 (%)
2.0558-2.1072	0.3756	129	0.2937	3850	X-RAY DIFFRACTION	93
2.1072-2.1642	0.3197	137	0.2692	4118	X-RAY DIFFRACTION	100
2.1642-2.2279	0.3207	142	0.2694	4126	X-RAY DIFFRACTION	100
2.2279-2.2998	0.3648	141	0.3184	4114	X-RAY DIFFRACTION	100
2.2998-2.382	0.2423	141	0.2363	4143	X-RAY DIFFRACTION	100
2.382-2.4773	0.2829	138	0.2268	4129	X-RAY DIFFRACTION	100
2.4773-2.5901	0.2572	146	0.2141	4170	X-RAY DIFFRACTION	100
2.5901-2.7266	0.266	144	0.2198	4137	X-RAY DIFFRACTION	100
2.7266-2.8974	0.2659	144	0.2338	4148	X-RAY DIFFRACTION	100
2.8974-3.121	0.2836	146	0.2082	4212	X-RAY DIFFRACTION	100
3.121-3.435	0.2401	145	0.1867	4192	X-RAY DIFFRACTION	99
3.435-3.9317	0.2089	140	0.1551	4147	X-RAY DIFFRACTION	98
3.9317-4.9522	0.153	141	0.1244	4254	X-RAY DIFFRACTION	99
4.9522-41.3068	0.1577	149	0.1593	4466	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	8.1461	-4.0423	-0.8864	2.8675	1.8772	5.1397	-0.1369	-0.0752	-1.1542	0.0407	0.1999	-0.5903	0.6823	0.5344	0.1794	0.9207	0.0778	0.0569	0.5894	0.0094	0.7221	32.9789	-21.078	18.8944
2	8.1175	3.0397	1.0925	2.6301	1.2087	2.3221	0.1373	-0.4676	0.4176	0.5825	-0.1578	0.5497	0.1138	-0.1528	-0.0395	0.659	0.0258	0.1163	0.37	-0.029	0.4417	15.5574	-24.5419	21.0605
3	0.8981	-0.1661	-0.2041	1.3187	0.2476	1.6134	0.0484	0.0662	0.0423	0.1287	-0.0004	0.1444	-0.0949	-0.0947	-0.0429	0.448	0.0269	0.0302	0.3962	0.0109	0.4294	9.6617	-32.5293	1.9298
4	9.0736	6.2144	6.8099	8.3307	6.6799	6.0799	-0.0125	0.1577	0.1964	0.1592	-0.1788	0.5667	-0.1393	-0.3474	0.2259	0.37	0.0427	0.0984	0.397	0.029	0.4496	3.6266	-30.6575	4.0801
5	1.5321	0.6008	0.4405	4.6013	-0.8292	3.1062	0.1971	0.3486	0.403	0.2814	-0.0158	0.2987	-0.413	-0.326	-0.213	0.5263	0.0929	0.1516	0.4335	0.0152	0.5843	6.3276	-18.7254	8.1977
6	2.0848	0.6393	-0.3226	2.5087	1.0453	2.2754	0.075	0.1009	0.4139	0.0157	0.0256	0.1098	-0.4548	0.1636	-0.0647	0.591	-0.0028	0.0278	0.3956	-0.0071	0.4928	25.7015	-18.7937	10.9896
7	4.3515	-0.9105	2.9906	1.0243	-0.6355	2.0846	0.3912	0.5815	-0.6848	-0.6202	0.2755	-0.3942	0.5123	1.2319	-0.5166	0.7149	-0.026	0.0161	0.7656	-0.1603	0.6367	20.0078	-58.1224	-39.2111
8	1.7207	-0.4768	0.2481	8.7868	1.5264	2.5933	-0.2513	0.4219	-0.0388	-0.5771	0.2776	0.2177	-0.2718	0.2664	-0.0384	0.4325	-0.0399	-0.032	0.7192	0.0443	0.4057	10.8281	-37.2954	-42.8668
9	1.2291	-0.05	0.4135	0.7829	-0.1115	2.9929	-0.0985	0.1227	0.0384	-0.0114	0.0761	0.0402	-0.2435	-0.1385	0.0287	0.3874	0.0023	-0.0146	0.4713	0.0133	0.4192	11.5913	-32.2821	-23.8292
10	1.9361	-0.6656	-0.4612	4.0888	5.3774	7.157	-0.2114	0.2199	0.1398	0.3015	0.1495	0.1684	-0.1473	-0.2284	0.0912	0.4337	0.0447	-0.0112	0.5206	0.0496	0.4329	6.0153	-28.8069	-27.7914
11	1.974	1.4016	-0.9869	0.9815	-0.8816	2.9909	-0.1455	0.155	0.0162	0.0403	0.0936	0.3094	0.0377	-0.5939	0.0023	0.3347	-0.0081	0.022	0.6506	0.0143	0.4408	-0.1127	-39.1773	-32.0225
12	2.1932	-0.2491	0.9235	2.6113	0.5365	2.611	0.0669	0.099	-0.3214	0.2841	0.051	0.2023	0.6667	-0.6257	-0.1035	0.4936	-0.0713	0.0397	0.589	-0.0248	0.5018	13.3131	-52.6141	-33.2996
13	8.9597	-0.1928	1.3572	9.5993	0.2425	2.0397	0.1618	0.1604	0.2102	0.1005	-0.3659	0.2402	-0.0963	-0.3598	0.0696	0.8503	0.0096	0.0835	0.4444	0.0549	0.6547	9.1882	-52.7615	19.082
14	6.6083	4.3841	-1.2163	5.9361	-1.5383	2.3618	0.076	-0.5795	-0.0932	0.4431	-0.092	-0.0296	0.048	-0.0779	0.045	0.7567	0.0024	-0.0613	0.4198	0.013	0.411	24.1986	-45.2408	22.5455
15	1.2526	0.2773	0.0396	1.4447	-0.1075	1.9061	0.0679	0.0102	-0.0909	0.2301	-0.0414	-0.0883	0.0681	0.1429	-0.0224	0.447	0.0327	-0.0309	0.3594	-0.0117	0.408	31.0904	-39.7014	3.2733
16	2.2661	2.2338	-1.529	4.6101	-1.6683	2.5978	0.1257	-0.0342	-0.3115	0.1977	-0.0355	-0.2168	0.334	0.3804	-0.1158	0.472	0.105	-0.1056	0.4375	-0.0242	0.4601	35.7325	-48.9841	6.0274
17	2.496	-0.1855	0.5963	0.0791	-0.3088	0.8523	0.2585	-0.0143	-0.5166	0.1411	-0.0215	-0.1721	0.4042	0.0107	-0.2581	0.6133	0.0422	-0.0396	0.3508	-0.0079	0.4965	23.9537	-51.4751	11.8516
18	1.0236	-0.07	-0.536	2.3048	-0.9556	0.8533	-0.1207	0.3969	-0.3664	-0.177	0.171	0.3607	0.1724	-0.4891	-0.0378	0.6391	-0.0384	0.0339	0.3986	-0.0016	0.5063	11.9889	-53.0898	12.2898
19	4.4135	-0.8219	-0.7887	0.2128	0.1461	0.1404	0.2711	1.5878	0.8239	-0.4669	0.0267	0.7679	-0.1495	-0.2216	-0.2908	0.7991	-0.053	-0.1451	0.8398	0.1719	0.7948	22.2985	-16.1187	-40.6289
20	1.512	-1.1504	-0.0302	5.0222	0.1401	1.9773	0.0189	0.3499	0.0363	-0.2025	-0.2713	-0.0489	-0.0906	0.1196	0.2475	0.4055	-0.0363	0.0051	0.6146	-0.0545	0.421	32.8319	-35.6284	-41.7838
21	2.4007	-0.1715	0.1338	3.7535	-0.529	1.5327	-0.273	0.2108	-0.4426	-0.0154	0.0351	-0.2531	0.5163	0.3094	0.2298	0.5612	-0.0126	0.0814	0.524	-0.0325	0.5013	30.6725	-50.5942	-28.4026
22	0.9686	0.2259	-0.4734	0.6243	0.4896	2.6917	-0.071	0.1561	-0.0414	0.0919	0.1092	-0.0418	0.2113	0.1815	-0.0224	0.3873	0.0332	0.0047	0.4839	-0.0246	0.4345	31.8544	-40.4405	-22.6551
23	3.5518	1.5121	1.2225	2.385	0.779	5.8499	-0.069	0.1574	-0.1164	0.185	0.3094	-0.6682	-0.208	1.0139	-0.1761	0.363	0.0045	0.0137	0.63	-0.0555	0.4547	43.2938	-33.5201	-30.6152
24	1.8004	0.3215	-0.8949	1.8971	-0.7062	1.869	0.0923	0.3168	0.3096	0.356	0.0266	-0.0438	-0.6323	0.2751	-0.1488	0.5977	-0.1355	-0.0321	0.6183	0.0459	0.4884	29.6817	-21.2892	-33.4884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 0:5)
2	X-RAY DIFFRACTION	2	(chain A and resid 6:23)
3	X-RAY DIFFRACTION	3	(chain A and resid 24:118)
4	X-RAY DIFFRACTION	4	(chain A and resid 119:129)
5	X-RAY DIFFRACTION	5	(chain A and resid 130:149)
6	X-RAY DIFFRACTION	6	(chain A and resid 150:180)
7	X-RAY DIFFRACTION	7	(chain B and resid 0:6)
8	X-RAY DIFFRACTION	8	(chain B and resid 7:30)
9	X-RAY DIFFRACTION	9	(chain B and resid 31:118)
10	X-RAY DIFFRACTION	10	(chain B and resid 119:129)
11	X-RAY DIFFRACTION	11	(chain B and resid 130:149)
12	X-RAY DIFFRACTION	12	(chain B and resid 150:179)
13	X-RAY DIFFRACTION	13	(chain C and resid 0:8)
14	X-RAY DIFFRACTION	14	(chain C and resid 9:21)
15	X-RAY DIFFRACTION	15	(chain C and resid 22:118)
16	X-RAY DIFFRACTION	16	(chain C and resid 119:140)
17	X-RAY DIFFRACTION	17	(chain C and resid 141:161)
18	X-RAY DIFFRACTION	18	(chain C and resid 162:180)
19	X-RAY DIFFRACTION	19	(chain D and resid 0:4)
20	X-RAY DIFFRACTION	20	(chain D and resid 5:30)
21	X-RAY DIFFRACTION	21	(chain D and resid 31:41)
22	X-RAY DIFFRACTION	22	(chain D and resid 42:129)
23	X-RAY DIFFRACTION	23	(chain D and resid 130:150)
24	X-RAY DIFFRACTION	24	(chain D and resid 151:179)

-
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

-
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

-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

-
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