PDB-4paw: Structure of hypothetical protein HP1257.

ID or keywords:

Entry

Database: PDB / ID: 4paw

Title

Structure of hypothetical protein HP1257.

Components

Orotate phosphoribosyltransferase

Keywords

TRANSFERASE /

hypothetical protein

Function / homology

Function and homology information

UMP biosynthetic process /

orotate phosphoribosyltransferase /

orotate phosphoribosyltransferase activity / nucleoside metabolic process / pyrimidine nucleobase biosynthetic process / 'de novo' UMP biosynthetic process / magnesium ion binding
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.23 Å

Authors

Battaile, K.P. / Lam, R. / Lam, K. / Romanov, V. / Jones, K. / Soloveychik, M. / Pai, E.F. / Chirgadze, N.Y.

Citation

Journal: To Be Published
Title: Structure of hypothetical protein HP1257.
Authors: Battaile, K.P. / Lam, R. / Lam, K. / Romanov, V. / Jones, K. / Soloveychik, M. / Pai, E.F. / Chirgadze, N.Y.

History

Deposition	Apr 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_keywords Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_keywords.text

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4paw.cif.gz	169.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4paw.ent.gz	134.6 KB	Display	PDB format
PDBx/mmJSON format	4paw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pa/4paw ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4paw	HTTPS FTP

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Related structure data

Similar structure data	1p4b-d 4p3h-1 1a7o-d 5n7b-d 3auv-2 3dkr-d 4doo-1 1a7p-d 5uvp-1 6qf6-3 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 (4) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Orotate phosphoribosyltransferase

B: Orotate phosphoribosyltransferase

hetero molecules

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

1

A: Orotate phosphoribosyltransferase

hetero molecules

defined by author
24.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Orotate phosphoribosyltransferase

hetero molecules

defined by author
24.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	69.060, 69.060, 192.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Orotate phosphoribosyltransferase / / OPRTase Mass: 24647.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: pyrE / Production host: Escherichia coli (E. coli) References: UniProt: P56162, orotate phosphoribosyltransferase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-SCN / THIOCYANATE ION / Thiocyanate Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.32 Å³/Da / Density % sol: 47.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaSCN, 21% PEG 3350, 0.1M NaHEPES

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.23→192 Å / Num. obs: 23753 / % possible obs: 100 % / Redundancy: 12.6 % / B_iso Wilson estimate: 43.92 Å² / Net I/σ(I): 24.9

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Processing

Software

Name: BUSTER / Version: 2.10.0 / Classification: refinement

Refinement

Resolution: 2.23→64.99 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.9158 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU R_free Blow DPI: 0.201 / SU R_free Cruickshank DPI: 0.198

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2439	1209	5.14 %	RANDOM
R_work	0.1909	-	-	-
obs	0.1934	23513	99.84 %	-

Displacement parameters

B_iso mean: 47.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.2249 Å²	0 Å²	0 Å²
2-	-	-4.2249 Å²	0 Å²
3-	-	-	8.4499 Å²

Refine analyze

Luzzati coordinate error obs: 0.319 Å

Refinement step

Cycle: 1 / Resolution: 2.23→64.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3014	0	15	102	3131

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	3078	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.13	4147	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1090	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		70	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		448	HARMONIC	5
X-RAY DIFFRACTION	t_it		3078	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		1	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	3.17
X-RAY DIFFRACTION	t_other_torsion	18.59
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		404	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies		1	HARMONIC	1
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3498	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.23→2.33 Å / Total num. of bins used: 12

	R_factor	Num. reflection	% reflection
R_free	0.2807	154	5.58 %
R_work	0.2293	2605	-
all	0.2322	2759	-
obs	-	-	99.84 %

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	10.6331	0.0134	1.4195	10.011	0.9875	5.1496	-0.0088	-0.8273	-0.4946	0.5601	0.2671	0.2694	0.4925	0.2382	-0.2583	-0.0997	0.1548	0.0767	0.0539	0.1355	-0.1206	28.4368	-3.7691	47.2119
2	0	-0.1758	1.0621	12.0784	-4.6434	1.818	0.1382	-0.1254	-0.499	-0.4444	-0.0395	-0.6989	0.3396	0.138	-0.0987	0.018	0.0967	-0.0288	-0.0331	0.0469	0.1682	32.0593	-12.4605	38.9593
3	0.3921	2.8505	2.3354	5.7129	-0.222	4.0701	-0.0686	-0.5109	0.3006	0.866	-0.0373	-0.274	-0.423	0.0275	0.1059	0.0913	0.1145	-0.05	0.0213	-0.0155	-0.131	37.8518	8.3376	44.6556
4	5.2278	-0.3603	0.1048	3.8086	-2.986	3.9348	-0.2128	-0.0441	-0.1189	0.162	0.0457	-0.2885	-0.2968	0.1423	0.1671	-0.1251	0.04	-0.0156	-0.0296	0.0299	-0.0764	42.2874	7.5513	35.0982
5	5.5626	-1.8025	1.3097	0.2656	-1.4303	8.975	0.0007	0.3995	-0.3235	-0.6048	-0.0976	-0.115	0.8632	0.2559	0.0969	-0.0016	0.0229	0.0832	-0.0262	0.0297	-0.0556	43.3056	1.3396	24.2193
6	4.0009	0.3063	0.735	0	-1.1839	6.7283	0.0143	0.1033	-0.1639	-0.3048	-0.2605	-0.7787	-0.1	0.5125	0.2462	-0.0862	0.004	0.0758	0.0463	0.1058	0.0352	49.6825	8.1942	23.2786
7	4.8087	0.2524	-2.9572	3.1273	-3.3217	6.172	-0.2122	-0.0433	-0.295	-0.0815	-0.0205	-0.077	0.0861	0.1487	0.2327	-0.1479	0.0594	0.0116	-0.0129	0.037	-0.0417	44.5644	-1.3112	36.2218
8	0	-0.8132	1.5619	2.6881	-0.3788	1.3707	0.0224	0.2395	-0.0688	-0.2766	-0.2666	-0.5971	0.6158	0.159	0.2442	-0.0475	0.1518	0.128	0.0801	0.0049	0.092	50.7267	-3.434	28.4172
9	4.9789	-1.1185	-1.057	2.9335	-0.7372	5.6387	-0.1705	-0.2295	-0.3389	0.1945	-0.1204	-0.4152	-0.0716	0.5137	0.2909	-0.2974	0.1333	-0.0181	-0.1028	0.0624	-0.1405	47.3944	-1.9956	39.651
10	6.3087	-0.0182	-1.5469	6.0356	-3.5925	3.2922	-0.1555	-0.5929	-0.6024	0.3371	-0.1968	-0.606	0.003	0.503	0.3524	-0.1277	0.1128	0.0087	0.0295	0.1392	0.0383	47.5256	-6.1284	45.5541
11	6.5684	5.8614	2.8123	8.0595	4.8175	4.1548	-0.0382	0.0684	-0.5933	-0.1744	0.1059	-0.1923	0.1709	0.2339	-0.0677	0	0.1839	-0.0486	-0.2351	0.1383	0.3098	34.1357	-23.6947	41.5423
12	0.6042	-0.4439	-1.1859	4.0893	-3.9727	4.4985	-0.0018	-0.3053	0.4485	-0.0354	0.2352	0.0822	-0.6152	0.5117	-0.2334	0.0558	-0.1126	-0.0106	-0.0288	-0.0406	-0.058	38.1612	23.2563	17.8551
13	0	0.0686	-0.1565	0	-0.2743	8.2568	-0.0937	-0.0559	-0.1566	-0.1383	0.0708	-0.0335	0.2969	-0.0137	0.0229	0.0484	-0.0499	0.0409	-0.0259	-0.0032	-0.075	40.4198	14.8371	10.7427
14	4.2908	1.3962	1.5488	3.2056	-1.2087	2.0295	-0.0309	-0.3849	0.5137	0.136	0.0304	-0.0196	-0.2727	-0.1514	0.0005	-0.0065	0.0732	0.0215	-0.0676	0.0044	-0.1308	26.7309	20.0565	28.1735
15	2.6791	-0.3658	0.3087	2.0248	-0.8309	4.6498	-0.145	0.0856	-0.0797	0.1462	0.0986	-0.0171	-0.0201	-0.0996	0.0463	-0.0759	0.0148	0.0221	0.0388	0.04	-0.0752	24.3889	6.9141	27.7525
16	0.0878	-1.7671	2.4697	10.8239	-0.8386	3.4709	-0.0701	0.1497	-0.8303	-0.1855	0.1074	-0.0412	0.5458	-0.0005	-0.0373	0.0325	-0.0514	0.0236	0.1417	0.0015	-0.0077	21.3414	-4.837	26.4307
17	3.3928	-0.1175	0.6226	1.8862	-2.4996	3.4962	-0.0608	0.2313	-0.1199	-0.3319	-0.1091	0.1691	-0.0643	0.056	0.1698	-0.0222	-0.0049	0.0147	0.0651	0.0067	-0.0651	23.8877	8.7665	19.0579
18	0.496	1.1009	-0.7321	3.3027	1.6717	3.4835	0.0617	0.3475	0.0278	-0.3575	-0.1611	0.19	0.3135	-0.4514	0.0993	0.0391	-0.0124	-0.0173	0.1714	0.0096	-0.0386	19.7906	-0.6066	17.4297
19	2.5508	1.3273	-1.4646	4.1658	-1.681	4.8391	-0.0927	0.3668	0.1137	-0.4347	0.1872	0.3877	-0.1345	-0.2742	-0.0945	-0.1001	-0.0058	-0.0435	0.0684	0.0652	-0.1034	19.4254	13.0886	13.9522
20	5.1864	-1.4457	-4.2687	1.7433	1.2315	4.5123	0.0583	-0.3217	-0.0065	-0.0898	0.1713	-0.1984	-0.319	0.0688	-0.2296	-0.0165	-0.0873	0.0139	-0.0619	-0.0176	-0.159	39.3481	18.2695	3.1022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|0 - 15}
2	X-RAY DIFFRACTION	2	{A\|16 - 38}
3	X-RAY DIFFRACTION	3	{A\|39 - 56}
4	X-RAY DIFFRACTION	4	{A\|57 - 81}
5	X-RAY DIFFRACTION	5	{A\|82 - 96}
6	X-RAY DIFFRACTION	6	{A\|97 - 107}
7	X-RAY DIFFRACTION	7	{A\|108 - 119}
8	X-RAY DIFFRACTION	8	{A\|120 - 131}
9	X-RAY DIFFRACTION	9	{A\|132 - 151}
10	X-RAY DIFFRACTION	10	{A\|152 - 175}
11	X-RAY DIFFRACTION	11	{A\|176 - 196}
12	X-RAY DIFFRACTION	12	{B\|1 - 15}
13	X-RAY DIFFRACTION	13	{B\|16 - 38}
14	X-RAY DIFFRACTION	14	{B\|39 - 55}
15	X-RAY DIFFRACTION	15	{B\|56 - 91}
16	X-RAY DIFFRACTION	16	{B\|92 - 107}
17	X-RAY DIFFRACTION	17	{B\|108 - 119}
18	X-RAY DIFFRACTION	18	{B\|120 - 131}
19	X-RAY DIFFRACTION	19	{B\|132 - 170}
20	X-RAY DIFFRACTION	20	{B\|171 - 196}

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