PDB-3kb8: 2.09 Angstrom resolution structure of a hypoxanthine-guanine phos...

ID or keywords:

Entry

Database: PDB / ID: 3kb8

Title

2.09 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor' in complex with GMP

Components

Hypoxanthine phosphoribosyltransferase

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE /

Hypoxanthine-Guanine Phosphoribosyltransferase /

Structural Genomics /

Infectious Diseases / Center for Structural Genomics of Infectious Diseases /

Glycosyltransferase / CSGID

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity /

hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage /

nucleotide binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Bacillus anthracis str. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.09 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor' in complex with GMP
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Oct 20, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3kb8.cif.gz	172.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3kb8.ent.gz	137.5 KB	Display	PDB format
PDBx/mmJSON format	3kb8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kb/3kb8 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kb8	HTTPS FTP

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Related structure data

Related structure data	3h83S 3hvu S: Starting model for refinement
Similar structure data	3h83-d 4rhu-1 3t0c-d 1yfz-1 3zpx-d 2pq5-d 5kny-d 5knp-d 2nq5-d 6b9s-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP01892

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (7) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Hypoxanthine phosphoribosyltransferase

B: Hypoxanthine phosphoribosyltransferase

C: Hypoxanthine phosphoribosyltransferase

D: Hypoxanthine phosphoribosyltransferase

hetero molecules

95 kDa, 4 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)	54.220, 80.477, 120.236
Angle α, β, γ (deg.)	90.00, 101.24, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein

Hypoxanthine phosphoribosyltransferase /

Hypoxanthine-guanine phosphoribosyltransferase

Mass: 22975.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus anthracis str. (bacteria) / Strain: 'Ames Ancestor' / Gene: BAA_0076, hpt, hpt-1 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3P9L0, UniProt: B9ZW32*PLUS,

hypoxanthine phosphoribosyltransferase

#2: Polysaccharide

beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /

Type: oligosaccharide

, Oligosaccharide

/ Class: Nutrient

/ Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References:

sucrose

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Non-polymers , 5 types, 271 molecules

#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.8 Å³/Da / Density % sol: 56.07 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: The Classics II Suite, condition B6, mixed at 1:1 v/v ratio with the protein at 7.4 mg/mL in 0.5 M NaCl, 5 mM BME, 1 mM GMP, 1 mM MgCl2, 10 mM Tris/HCl pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Jul 22, 2009 / Details: Be Lenses/Diamond Laue Mono
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: 2.09→50 Å / Num. all: 56550 / Num. obs: 56550 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / R_merge(I) obs: 0.101 / Net I/σ(I): 9.61
Reflection shell	Resolution: 2.09→2.13 Å / Redundancy: 3 % / R_merge(I) obs: 0.539 / Mean I/σ(I) obs: 2.66 / Num. unique all: 2964 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3H83

3h83

Resolution: 2.09→30.08 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.925 / SU B: 9.431 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2431	2830	5 %	RANDOM
R_work	0.20385	-	-	-
obs	0.20582	53702	93.92 %	-
all	-	53702	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 24.226 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0 Å²	-0 Å²	-2.59 Å²
2-	-	0.33 Å²	-0 Å²
3-	-	-	-1.33 Å²

Refinement step

Cycle: LAST / Resolution: 2.09→30.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5921	0	190	253	6364

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6316
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4174
X-RAY DIFFRACTION	r_angle_refined_deg	1.696	2.034	8579
X-RAY DIFFRACTION	r_angle_other_deg	0.889	3	10311
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.23	5	756
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.86	25.08	250
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.261	15	1138
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.432	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1015
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6652
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1148
X-RAY DIFFRACTION	r_mcbond_it	1.032	1.5	3755
X-RAY DIFFRACTION	r_mcbond_other	0.306	1.5	1533
X-RAY DIFFRACTION	r_mcangle_it	1.804	2	6108
X-RAY DIFFRACTION	r_scbond_it	2.944	3	2561
X-RAY DIFFRACTION	r_scangle_it	4.359	4.5	2471

LS refinement shell

Resolution: 2.09→2.144 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	207	-
R_work	0.224	4184	-
obs	-	4184	98.9 %

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	1.7036	-0.3383	0.0748	0.9959	0.1773	0.2616	0.0316	0.0186	0.0553	-0.0449	0.0495	-0.2063	0.0069	0.184	-0.0811	0.1159	0.0043	0.0053	0.1463	-0.0141	0.1756	59.3107	3.7748	49.8421
2	0.8459	0.328	-0.226	1.2332	0.1988	2.2944	0.0018	0.0429	0.038	0.0227	-0.0006	0.0689	-0.0002	0.0116	-0.0012	0.0269	0.0036	0.0065	0.0037	0.0072	0.0964	34.863	7.7065	48.4366
3	0.7615	0.0544	0.3048	0.5688	0.1242	2.2341	0.0131	0.0471	0.007	-0.0727	0.0417	0.0177	-0.1899	-0.0146	-0.0548	0.0375	0.0028	0.0102	0.0073	0.0059	0.0764	35.5073	14.8283	41.2921
4	1.7039	0.7225	0.1774	2.283	1.398	1.9739	0.1152	0.0071	0.1255	-0.2005	-0.0227	-0.1707	-0.3642	0.2703	-0.0925	0.0817	-0.0539	0.0404	0.0788	0.0014	0.1455	55.2912	10.4534	51.5219
5	3.9289	-1.7005	1.8177	1.7345	-0.5507	1.4572	0.052	-0.1934	0.0415	-0.0021	-0.0097	0.1802	0.02	-0.1457	-0.0423	0.0733	-0.0123	0.0311	0.0521	0.0196	0.1119	26.6368	-5.3102	57.029
6	0.3802	0.2559	-0.1772	0.8498	-0.5702	1.589	0.0199	0.0931	-0.1116	-0.0636	0.0132	-0.0413	0.0274	0.0027	-0.0332	0.0511	0.0099	0.0185	0.0284	-0.0212	0.1053	47.019	-7.9368	46.632
7	0.6937	-0.0968	-0.4828	0.388	-0.5356	2.7731	0.0026	0.0736	-0.0843	-0.071	0.0053	0.0616	0.271	-0.0789	-0.0078	0.066	-0.002	-0	0.0085	-0.0064	0.0873	45.075	-15.2291	41.6181
8	3.4915	0.0656	-0.8016	1.8854	-0.4096	2.0792	0.147	0.1053	-0.2783	-0.1858	-0.0285	0.3126	0.2135	-0.2272	-0.1185	0.0591	-0.0138	-0.0306	0.0286	0.0068	0.1509	25.2219	-8.9441	50.9315
9	3.6658	3.2666	0.1414	9.3972	2.3534	2.0341	-0.0675	0.336	0.1019	-0.6129	0.0523	-0.3101	-0.1796	0.1432	0.0152	0.1818	-0.0268	0.0382	0.1952	0.0713	0.0502	54.7345	8.3338	-2.1911
10	1.7461	0.3447	-0.1587	1.8895	0.6599	1.6466	-0.047	0.1603	-0.1161	-0.1218	-0.0567	0.0266	0.0698	0.0333	0.1037	0.1054	0.0043	0.0025	0.1222	-0.0283	0.0585	42.1909	-10.3115	4.8974
11	0.5385	-0.063	-0.2388	0.6538	-0.2616	2.1128	-0.0237	0.1112	-0.0545	-0.0771	0.0156	-0.08	0.1118	0.2629	0.0081	0.0917	0.0206	0.0235	0.1125	-0.0207	0.0868	51.8076	-9.8446	17.3136
12	1.8455	0.2625	-1.6945	1.1067	-0.1811	1.7784	-0.073	-0.0601	0.0192	0.0809	0.012	-0.1694	0.0389	0.2473	0.061	0.1166	-0.0311	-0.0044	0.1763	0.0565	0.0993	55.9546	9.0668	7.0986
13	2.237	2.799	0.3681	6.7254	0.2813	0.5905	-0.1734	0.3241	0.0173	-0.5049	0.1029	0.1458	0.0202	-0.005	0.0704	0.1529	-0.0145	-0.0187	0.1969	-0.0145	0.0293	30.3369	1.3082	-2.0618
14	0.4095	-0.2599	0.0729	0.5569	-0.0411	2.2132	-0.003	0.1333	0.0173	-0.0881	-0.0475	0.0149	-0.0383	-0.0728	0.0505	0.0917	-0.008	-0.0039	0.1115	0.0119	0.0897	37.9713	8.2283	12.2856
15	0.3451	-0.3327	0.2698	0.6677	0.2375	2.32	0.0315	0.0428	0.0005	-0.0526	0.0015	0.0656	-0.1073	-0.2299	-0.033	0.0844	0.0136	-0.0144	0.1007	0.0153	0.0788	30.4965	11.5194	18.6407
16	0.7127	0.494	0.1169	1.7457	0.6458	0.4988	-0.0154	0.0411	-0.0263	0.0192	-0.0493	0.2972	-0.0319	-0.1809	0.0647	0.1414	-0.0051	-0.0015	0.1893	-0.0237	0.1125	24.689	-2.7943	6.8494
17	0.2064	0.071	-1.4441	0.0879	-0.6185	10.3399	-0.0986	-0.1343	-0.0711	-0.0911	-0.1099	0.1323	0.8491	1.1025	0.2085	0.274	0.0463	-0.0673	0.3556	-0.1195	0.4224	49.3059	15.1135	45.1082
18	10.3447	3.096	2.8514	4.9047	1.6996	0.9663	0.0001	0.3352	-0.2193	-0.5974	-0.0659	0.3888	-0.1356	0.057	0.0658	0.2316	-0.0013	-0.0622	0.1337	0.0574	0.1685	32.7177	-14.8463	44.6592
19	11.436	-10.4304	6.7508	24.6834	0.984	7.3478	0.1498	-0.3282	-0.1417	0.5692	-0.1882	0.3978	0.4124	-0.4115	0.0384	0.1175	-0.0964	0.0769	0.1576	-0.0339	0.0998	35.068	19.8266	59.7657
20	14.1784	-5.4734	14.6672	31.5849	21.9527	41.0485	0.4283	-0.203	-0.1599	0.0824	-1.9268	1.9304	0.7917	-2.0019	1.4985	0.2247	0.0737	0.0353	0.3889	-0.043	0.3438	19.9077	7.5153	-2.5218
21	1.0352	2.0804	4.9121	4.1969	9.9051	23.3788	0.2755	0.0071	-0.1056	0.3543	0.0336	-0.1685	0.849	-0.0973	-0.309	0.3038	0.0468	0.0424	0.358	-0.0849	0.6058	60.71	-6.8594	-2.886

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-23 - 16
2	X-RAY DIFFRACTION	2	A	17 - 78
3	X-RAY DIFFRACTION	3	A	79 - 147
4	X-RAY DIFFRACTION	4	A	148 - 179
5	X-RAY DIFFRACTION	5	B	-8 - 21
6	X-RAY DIFFRACTION	6	B	22 - 78
7	X-RAY DIFFRACTION	7	B	79 - 151
8	X-RAY DIFFRACTION	8	B	152 - 180
9	X-RAY DIFFRACTION	9	C	0 - 16
10	X-RAY DIFFRACTION	10	C	17 - 61
11	X-RAY DIFFRACTION	11	C	62 - 150
12	X-RAY DIFFRACTION	12	C	151 - 179
13	X-RAY DIFFRACTION	13	D	0 - 30
14	X-RAY DIFFRACTION	14	D	31 - 74
15	X-RAY DIFFRACTION	15	D	75 - 137
16	X-RAY DIFFRACTION	16	D	138 - 179
17	X-RAY DIFFRACTION	17	A	266
18	X-RAY DIFFRACTION	18	B	267
19	X-RAY DIFFRACTION	19	A	268
20	X-RAY DIFFRACTION	20	D	270
21	X-RAY DIFFRACTION	21	C	271

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Protein / Sugars , 2 types, 7 molecules ABCD

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Non-polymers , 5 types, 271 molecules

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