PDB-7kl7: Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosylt...

ID or keywords:

Entry

Database: PDB / ID: 7kl7

Title

Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase

Components

Phosphoribosyltransferase

Keywords

TRANSFERASE / Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase Drug discovery Nucleoside phosphates

Function / homology

Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Phosphoribosyltransferase

Function and homology information

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.47 Å

Authors

Guddat, L.W. / Keough, D.T.

Funding support

Australia, 1items

Citation

Journal: J.Med.Chem. / Year: 2021
Title: Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections.
Authors: Keough, D.T. / Wun, S.J. / Baszczynski, O. / Eng, W.S. / Spacek, P. / Panjikar, S. / Naesens, L. / Pohl, R. / Rejman, D. / Hockova, D. / Ferrero, R.L. / Guddat, L.W.

History

Deposition	Oct 29, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 5, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 12, 2021	Group: Refinement description / Category: software
Revision 1.2	May 26, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kl7.cif.gz	172 KB	Display	PDBx/mmCIF format
PDB format	pdb7kl7.ent.gz	112.5 KB	Display	PDB format
PDBx/mmJSON format	7kl7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7kl7_validation.pdf.gz	442.6 KB	Display	wwPDB validaton report
Full document	7kl7_full_validation.pdf.gz	446 KB	Display
Data in XML	7kl7_validation.xml.gz	17 KB	Display
Data in CIF	7kl7_validation.cif.gz	25 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kl/7kl7 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/7kl7	HTTPS FTP

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Related structure data

Related structure data	7kl6C C: citing same article (ref.)
Similar structure data	7kl6-d 2xzj-2 6uob-1 3znr-3 5ef7-2 6uo5-d 1f76-1 2z2b-d 1f76-4 5z3f-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (3)

Deposited unit

A: Phosphoribosyltransferase

B: Phosphoribosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	40.201, 51.544, 82.687
Angle α, β, γ (deg.)	90.000, 96.092, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Phosphoribosyltransferase / Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase Mass: 18512.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BXP09_04485, CV723_04510 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2L2I2A6, Transferases; Glycosyltransferases
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.54 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane, pH 5.5, 0.2 M ammonium sulfate, 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
Detector	Type: BRUKER SMART 6000 / Detector: CCD / Date: Feb 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95365 Å / Relative weight: 1
Reflection	Resolution: 1.47→43.67 Å / Num. obs: 57196 / % possible obs: 99 % / Redundancy: 9 % / B_iso Wilson estimate: 15.18 Å² / CC_1/2: 0.8 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.47→11.49 Å / Num. unique obs: 256 / CC_1/2: 0.7

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
ARP/wARP		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MIR / Resolution: 1.47→34.54 Å / SU ML: 0.1894 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.0818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1943	2000	3.5 %
R_work	0.1722	55169	-
obs	0.173	57169	98.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.47→34.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2384	0	20	312	2716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0173	2474
X-RAY DIFFRACTION	f_angle_d	1.722	3361
X-RAY DIFFRACTION	f_chiral_restr	0.1248	380
X-RAY DIFFRACTION	f_plane_restr	0.0088	417
X-RAY DIFFRACTION	f_dihedral_angle_d	11.489	316

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 (%)
1.47-1.5	0.2979	133	0.2934	3645	X-RAY DIFFRACTION	91.99
1.5-1.54	0.2991	141	0.2661	3916	X-RAY DIFFRACTION	98.61
1.54-1.59	0.2698	141	0.233	3882	X-RAY DIFFRACTION	98.8
1.59-1.64	0.2776	141	0.2166	3900	X-RAY DIFFRACTION	99.04
1.64-1.7	0.2421	144	0.2028	3956	X-RAY DIFFRACTION	99.2
1.7-1.77	0.2344	143	0.1828	3946	X-RAY DIFFRACTION	99.42
1.77-1.85	0.2049	143	0.1788	3938	X-RAY DIFFRACTION	99.49
1.85-1.95	0.1918	143	0.1701	3960	X-RAY DIFFRACTION	99.83
1.95-2.07	0.1529	144	0.1531	3975	X-RAY DIFFRACTION	99.9
2.07-2.23	0.1857	145	0.1493	3997	X-RAY DIFFRACTION	99.98
2.23-2.45	0.1892	143	0.1608	3963	X-RAY DIFFRACTION	99.9
2.45-2.81	0.1854	145	0.1699	3989	X-RAY DIFFRACTION	99.9
2.81-3.53	0.179	145	0.1571	4017	X-RAY DIFFRACTION	99.78
3.53-34.54	0.1762	149	0.1636	4085	X-RAY DIFFRACTION	99.69

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	5.40904202607	1.42117868169	-0.521341804496	3.10541436346	0.151885708102	2.01410866426	-0.162151313799	0.420446603526	-0.499095970207	0.011988785299	0.0679338671678	-0.102121241886	0.47915593872	0.0638569240667	0.0632072116316	0.198245271273	0.0285500170942	-0.0196712034922	0.116137938493	-0.0324873340109	0.133613085301	31.6272062893	-9.66198109218	100.867734386
2	4.20904674179	-0.105329818946	-0.319742420881	1.5602869044	-0.187332335375	1.9817834631	-0.0218554501506	0.147228482084	0.119021345381	0.0427430891846	-0.00705000599575	-0.0425062147258	0.0110470561752	0.0458786028846	0.0391182813362	0.0824857564168	0.00564146160475	-0.00324396377697	0.0731322822743	-0.00601824159539	0.0593697199719	34.9585314958	2.27394110064	101.393466813
3	5.0188841314	-1.27820148191	0.430243382575	4.91153665948	-1.0955576733	4.04150802162	-0.0678078908987	0.106540528841	-0.0538202545143	0.0277655172853	0.139846295626	0.0921102727944	-0.265280550631	0.0683095404781	0.0434866268583	0.0511640168286	0.00362561500046	0.0122019669982	0.091273771455	-0.0195643175733	0.090404381332	34.8295570326	8.82141320092	98.6887081587
4	0.489342882292	-0.533027457697	0.781946460944	1.03503074855	-1.15619630588	1.46592760693	0.158087252413	0.564275450599	0.26688259542	-0.95360260261	-0.413635052098	0.913953325514	-0.487669171309	-1.33476205882	0.156978354249	0.454566831964	0.186577584193	-0.17591488775	0.722727561731	-0.0314407728665	0.405552153891	21.8931814606	12.6534630383	81.8701548308
5	4.38221284043	-0.627604924223	-0.124291843867	5.1022177423	-0.749941468595	3.20555412987	-0.0653007339513	-0.00317239302621	0.220187581357	0.0448574934119	0.0215842911357	-0.35018668042	-0.0990116076049	0.0401650483659	0.0580607329308	0.0960178423307	0.00177309015866	-0.00902353470735	0.121825765578	0.00348733542783	0.0464907013421	41.1548045427	9.42050154914	95.0607342978
6	7.14086709128	5.07688309751	-4.87165784174	8.52607010091	-5.08815780421	3.85988828712	-0.167597209015	0.272046498849	0.3186414703	-0.150087264951	0.0817767992401	0.473181308076	0.00798991048103	-0.497052455899	0.133457683541	0.18031751449	0.00473418815235	-0.0195574142824	0.172664267609	-0.0187571313383	0.176343267249	26.3209326097	-2.65146596322	88.2738252793
7	3.75357376241	5.1855906729	2.06514551236	8.08597455	1.59823197694	5.07372966407	-0.245688637388	0.417299403113	0.192759180326	-0.45387195606	0.0662120995738	-0.0507961292418	-0.0270959628721	0.141327527277	0.153233853322	0.158528375038	0.0175015241833	-0.0120797736227	0.166078919557	0.0252518143745	0.121533102959	35.7984060883	7.49127824344	84.8785895714
8	3.11324615724	2.35236477555	0.736225477475	4.21156012753	0.6112838535	2.29333668506	-0.056971358369	0.261437297609	-0.0853259558971	-0.164901582949	0.0168275619549	0.0814494412614	0.219166819576	-0.125999720091	0.00871154938418	0.137339075776	0.012553876341	0.00211227573238	0.156535340757	-0.0323777203736	0.0906059645504	33.0964070946	-4.07840484386	89.1239883483
9	3.89939808709	-3.80992558123	-4.86188850367	6.27961797589	3.88050362068	7.14553018863	0.0267236468074	0.670827292911	-0.382187624705	-0.241744060818	-0.2469054019	0.447117039134	-0.0529608779925	-0.75334937397	0.198071525561	0.125424575732	-0.0083826051089	-0.0437137366337	0.186372591444	-0.000390378680209	0.119612364938	14.8029978241	-2.6683329276	103.474627172
10	5.20908800541	-0.922845875863	-3.20795465376	4.36689502889	-0.267195069655	2.21749876757	-0.181800596081	-0.457479426927	0.218924445381	0.817681748817	0.0500926731511	-0.206734037418	-0.234324206269	0.548825792949	0.138272723124	0.255771563965	-0.0129157198397	-0.0502643983981	0.101469715641	0.00334068899813	0.0987397692531	29.472724901	0.625554961035	125.221235449
11	6.79542735588	-5.60041346126	1.51471249652	4.72303204352	-2.36284597581	2.88620195474	-0.110186836701	-0.288541744343	0.142321023212	0.275009777932	0.185383078462	0.152149555305	-0.1772845064	-0.239570966894	-0.0659540308753	0.0874304321804	-0.00119244888868	0.0132185707922	0.137948108503	-0.0132562721834	0.0992064647911	14.9038177554	8.05896526501	112.857066434
12	4.27802141114	-1.46410213653	1.71254988684	2.55916583062	-0.75507247456	2.58512026937	-0.0172766092939	0.172090317628	0.210778172856	-0.0567402055004	-0.0137537667128	-0.0913596082073	-0.0621658167939	-0.0445840073221	0.0235009626373	0.0840943843973	0.00544399414102	0.0165228127542	0.0903683285387	0.00426551422143	0.0712697609614	22.9572364686	10.0840079623	104.391555318
13	3.74550413673	4.64111387597	0.969993756158	6.04733028194	1.04696188275	4.45460546716	-0.22466023662	0.718437593355	0.0985818537409	-0.206919260025	0.297740645047	0.0999658827957	-0.209392190596	0.0965021309779	-0.121346697721	0.092665357911	0.032025327739	0.00262616165212	0.0974456341989	0.0124561751943	0.0952622425011	22.6713934684	13.1598452284	99.2892434593
14	0.907186844354	1.02821119207	-2.40117440126	8.38666173866	0.424977793093	7.7778751252	0.191757765907	-1.16857420776	0.737174289084	0.0907338201604	0.30308717936	-0.89312105606	-0.205798847718	1.04498071171	-0.333062426758	0.189981974433	-0.0270841965965	0.0572148039556	0.42506316157	-0.122056368509	0.287596322967	36.6886536347	20.0709182897	104.531453432
15	5.27823497034	-0.797784234666	-0.387216685885	6.0170641779	-3.06091291141	4.96557215651	0.280052242845	0.521915789473	0.269506157068	-0.185366023937	0.0855033419866	0.200243094647	-0.405255783873	-0.202789962401	-0.17343003259	0.172878849613	0.0411239873484	0.017386473733	0.131973990953	0.0322554804111	0.158887078128	21.4585445165	20.7115112296	100.581507253
16	7.18608290825	4.3482460467	3.02352772225	3.63353247934	3.62814828051	4.48861267345	0.0883043131656	-0.254758050795	-0.0881599021276	-0.0110234967377	-0.0618107334976	-0.421621776601	0.286084971146	0.133641020407	-0.0447108086022	0.184207574023	0.00311781931901	0.0218889646959	0.155354400377	-0.00261672556046	0.15627571244	30.3417806217	13.7461799327	118.282875777
17	4.85537107482	-2.40852599978	3.61251781149	7.36899562297	-5.41671339146	7.30043655885	-0.0374534777046	0.00800560174544	0.425679875918	0.0807806469003	0.193477017906	-0.345417728583	-1.18344458785	0.337949397219	-0.0288236760726	0.253299586358	-0.052473742214	0.0797662653246	0.119816080256	-0.0430901655781	0.226749054517	30.6817548611	24.4110562053	109.452445669
18	1.82347149646	0.897439935108	-0.311461140691	4.93226142363	-2.96238917462	4.52189150156	0.128909891101	0.0556237391072	0.418770640737	-0.0289406797248	0.135015930416	0.0697971332876	-0.476472536941	-0.0538509145597	-0.205865050624	0.193582658304	0.022375421031	0.0526124083877	0.0846272320201	0.024102684406	0.204654685045	22.0049815012	23.8189544197	106.030510299
19	2.49360825744	1.02295434647	1.11487142126	5.6473393528	0.449867949849	5.63704030798	0.0271798328222	-0.0884277235264	0.0537345147055	-0.0321133099796	-0.0472380869932	-0.179990227791	-0.0843487137452	0.0540144671337	0.00377874971573	0.111009366221	0.00369957606457	0.00372124525794	0.0870884960916	-0.0260299264855	0.080797296312	26.7060578518	16.6309395362	121.535924107
20	3.90455601288	-2.37386095689	2.67419611457	4.81533821837	-3.367867766	5.43690531997	-0.0917212712846	-0.268781023773	-0.143793573391	0.24884344031	0.150007710047	0.0101550894896	-0.139028731799	-0.421737740121	-0.0127378811918	0.131206185441	-0.0318647389614	-0.0116901428485	0.10664810651	-0.0365948552518	0.0943695389613	24.2144253327	10.8513477694	121.761995165
21	7.2071448543	0.214611796091	-1.13074430527	5.5746665901	0.0065448992921	4.24980167177	0.0870808495274	0.0142896715972	-0.55006459424	0.219783730843	-0.0724644264859	-0.268044430023	0.684617972061	0.192767440843	0.0106544155205	0.191366471277	0.0329790502731	-0.0271917122306	0.118609435901	0.00788460365538	0.127422783479	32.230311975	-4.14770160899	114.447559737

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 23 )	A	A	-1 - 23	1 - 26
2	2	chain 'A' and (resid 24 through 47 )	A	A	24 - 47	27 - 50
3	3	chain 'A' and (resid 48 through 59 )	A	A	48 - 59	51 - 62
4	4	chain 'A' and (resid 60 through 72 )	A	A	60 - 72	63 - 74
5	5	chain 'A' and (resid 73 through 88 )	A	A	73 - 88	75 - 90
6	6	chain 'A' and (resid 89 through 94 )	A	A	89 - 94	91 - 96
7	7	chain 'A' and (resid 95 through 107 )	A	A	95 - 107	97 - 109
8	8	chain 'A' and (resid 108 through 138 )	A	A	108 - 138	110 - 140
9	9	chain 'A' and (resid 139 through 153 )	A	A	139 - 153	141 - 155
10	10	chain 'B' and (resid -3 through 4 )	B	B	-3 - 4	1 - 8
11	11	chain 'B' and (resid 5 through 23 )	B	B	5 - 23	9 - 27
12	12	chain 'B' and (resid 24 through 46 )	B	B	24 - 46	28 - 50
13	13	chain 'B' and (resid 47 through 56 )	B	B	47 - 56	51 - 60
14	14	chain 'B' and (resid 57 through 76 )	B	B	57 - 76	61 - 70
15	15	chain 'B' and (resid 77 through 88 )	B	B	77 - 88	71 - 82
16	16	chain 'B' and (resid 89 through 94 )	B	B	89 - 94	83 - 88
17	17	chain 'B' and (resid 95 through 107 )	B	B	95 - 107	89 - 102
18	18	chain 'B' and (resid 108 through 117 )	B	B	108 - 117	103 - 112
19	19	chain 'B' and (resid 118 through 127 )	B	B	118 - 127	113 - 122
20	20	chain 'B' and (resid 128 through 138 )	B	B	128 - 138	123 - 133
21	21	chain 'B' and (resid 139 through 153 )	B	B	139 - 153	134 - 148

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