PDB-1rxu: E. coli uridine phosphorylase: thymidine phosphate complex

ID or keywords:

Entry

Database: PDB / ID: 1rxu

Title

E. coli uridine phosphorylase: thymidine phosphate complex

Components

Uridine phosphorylase

Keywords

TRANSFERASE / pentosyltransferase / uridine phosphorylase / thymidine / induced fit / specificity / potassium

Function / homology

Function and homology information

UMP catabolic process / uridine catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F.

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium
Authors: Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F.

History

Deposition	Dec 18, 2003	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 13, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	1rxu_validation.pdf.gz	623.7 KB	Display	wwPDB validaton report
Full document	1rxu_full_validation.pdf.gz	716.8 KB	Display
Data in XML	1rxu_validation.xml.gz	176.2 KB	Display
Data in CIF	1rxu_validation.cif.gz	217.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxu ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxu	HTTPS FTP

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Related structure data

Related structure data	1rxcC 1rxsC 1rxyC 1t0uC C: citing same article (ref.)
Similar structure data	1tgv-1 1u1f-d 4yjk-d 2rj3-d 4ip0-d 1tgy-1 5c80-d 1u1c-d 1rxy-1 4oeh-d Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uridine phosphorylase

B: Uridine phosphorylase

C: Uridine phosphorylase

D: Uridine phosphorylase

E: Uridine phosphorylase

F: Uridine phosphorylase

G: Uridine phosphorylase

H: Uridine phosphorylase

I: Uridine phosphorylase

J: Uridine phosphorylase

K: Uridine phosphorylase

L: Uridine phosphorylase

M: Uridine phosphorylase

N: Uridine phosphorylase

O: Uridine phosphorylase

P: Uridine phosphorylase

Q: Uridine phosphorylase

R: Uridine phosphorylase

hetero molecules

496 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uridine phosphorylase

B: Uridine phosphorylase

C: Uridine phosphorylase

D: Uridine phosphorylase

E: Uridine phosphorylase

F: Uridine phosphorylase

hetero molecules

defined by author&software
165 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Uridine phosphorylase

H: Uridine phosphorylase

I: Uridine phosphorylase

J: Uridine phosphorylase

K: Uridine phosphorylase

L: Uridine phosphorylase

hetero molecules

defined by author&software
165 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: Uridine phosphorylase

N: Uridine phosphorylase

O: Uridine phosphorylase

P: Uridine phosphorylase

Q: Uridine phosphorylase

R: Uridine phosphorylase

hetero molecules

defined by author&software
165 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	156.244, 97.655, 161.453
Angle α, β, γ (deg.)	90.00, 118.23, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 4 - 253 / Label seq-ID: 4 - 253

#1: Protein	Uridine phosphorylase / UrdPase / UPase Mass: 27189.055 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Details: This structure consists of eighteen monomers, all of which are in the closed conformation containing substrate (thymidine and phosphate). Due to the large size of the model it was refined ...Details: This structure consists of eighteen monomers, all of which are in the closed conformation containing substrate (thymidine and phosphate). Due to the large size of the model it was refined using a template model, and shell scripts were written to create the 18 monomer model from this input model using the ncs operators relating each monomer to the template. The 18 monomer model was then refined using refmac5 and ncs restraints were applied as a tight positional (0.05A) and loose thermal (5.0A3) restraints. These restraints, along with tls restraints where each monomer was treated as a separate tls domain, were applied with each monomer being restrained against the template model. Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UDP / Plasmid: pPROEX::pvdS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12758, uridine phosphorylase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₂O₅
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1062 / 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: 2.2 Å³/Da / Density % sol: 43.54 %
Crystal grow	Temperature: 289 K / Method: batch method under oil / pH: 7.5 Details: TRIS HCL, PEG4000, POTASSIUM ACETATE, THYMIDINE, POTASSIUM PHOSPHATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K

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Data collection

Diffraction	Mean temperature: 115 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 6, 2002 / Details: OSMIC
Radiation	Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3.1→41.89 Å / Num. all: 76410 / Num. obs: 76410 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / B_iso Wilson estimate: 61.398 Å² / R_merge(I) obs: 0.158 / Net I/σ(I): 4.7
Reflection shell	Resolution: 3.1→3.26 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.529 / Mean I/σ(I) obs: 1.4 / Num. unique all: 5116 / % possible all: 97

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing
REFMAC	5.1.24	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: A SINGLE HEXAMER (CHAINS ABCDEF) OF THE 5-FLUOROURACIL PHOSPHATE UP COMPLEX MODEL.

Resolution: 3.1→25 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.887 / SU B: 22.732 / SU ML: 0.397 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC (TLS REFINEMENT) / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.51 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS AND RESTRAINED REFINEMENT WAS CARRIED OUT USING REFMAC5.ALL 18 MONOMERS WERE REFINED USING NCS RESTRAINTS (TIGHT POSITIONAL (0.05A) AND LOOSE THERMAL (5.0A3) RESTRAINTS), AND EACH ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22945	3824	5 %	RANDOM
R_work	0.21167	-	-	-
all	0.21256	72181	-	-
obs	0.21256	72181	97.52 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 26.192 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.81 Å²	0 Å²	0.33 Å²
2-	-	1.57 Å²	0 Å²
3-	-	-	-0.45 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.5104 Å	0.491 Å
Luzzati d res low	-	25 Å

Refinement step

Cycle: LAST / Resolution: 3.1→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33840	0	405	1062	35307

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	34812
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.162	1.964	47304
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.707	5	4482
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	5652
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	25794
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	18128
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	1874
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.123	0.2	25
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.648	0.2	197
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.451	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.715	1.5	22302
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.447	2	35946
X-RAY DIFFRACTION	r_scbond_it	2.157	3	12510
X-RAY DIFFRACTION	r_scangle_it	4.054	4.5	11358
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 1939 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.04	0.05
2	B	tight positional	0.04	0.05
3	C	tight positional	0.04	0.05
4	D	tight positional	0.04	0.05
5	E	tight positional	0.04	0.05
6	F	tight positional	0.03	0.05
7	G	tight positional	0.04	0.05
8	H	tight positional	0.04	0.05
9	I	tight positional	0.03	0.05
10	J	tight positional	0.04	0.05
11	K	tight positional	0.04	0.05
12	L	tight positional	0.04	0.05
13	M	tight positional	0.04	0.05
14	N	tight positional	0.04	0.05
15	O	tight positional	0.03	0.05
16	P	tight positional	0.03	0.05
17	Q	tight positional	0.03	0.05
18	R	tight positional	0.03	0.05
1	A	tight thermal	0.06	0.5
2	B	tight thermal	0.07	0.5
3	C	tight thermal	0.07	0.5
4	D	tight thermal	0.06	0.5
5	E	tight thermal	0.05	0.5
6	F	tight thermal	0.05	0.5
7	G	tight thermal	0.07	0.5
8	H	tight thermal	0.06	0.5
9	I	tight thermal	0.06	0.5
10	J	tight thermal	0.06	0.5
11	K	tight thermal	0.07	0.5
12	L	tight thermal	0.07	0.5
13	M	tight thermal	0.06	0.5
14	N	tight thermal	0.06	0.5
15	O	tight thermal	0.05	0.5
16	P	tight thermal	0.05	0.5
17	Q	tight thermal	0.05	0.5
18	R	tight thermal	0.06	0.5

LS refinement shell

Resolution: 3.1→3.179 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	273	-
R_work	0.288	5116	-
obs	-	5116	95.38 %

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	1.01	0.228	0.1084	0.9407	0.6555	1.983	-0.0659	-0.3432	-0.096	0.24	-0.0105	-0.0922	0.1963	0.0804	0.0764	0.34	0.0787	-0.0144	0.2131	0.0148	0.1984	-1.312	-4.673	56.513
2	1.3577	0.2351	0.3988	0.7892	-0.1015	1.221	-0.0484	-0.1555	0.1861	0.08	0.0081	0.0637	-0.0126	-0.4348	0.0402	0.1465	0.0121	0.0589	0.179	-0.0457	0.1565	-19.757	0.728	40.682
3	1.9044	-1.3592	0.8527	0.9158	-1.2932	1.9013	0.0624	0.116	-0.1841	-0.1705	-0.1133	0.0207	0.3762	0.0218	0.0509	0.2162	0.008	0.0093	0.0286	-0.0249	0.1931	-13.661	-1.327	10.277
4	1.55	-0.1909	-0.6593	0.6582	0.6988	1.5783	-0.0487	0.1978	0.2929	-0.1807	-0.0398	-0.1972	-0.0067	0.1949	0.0885	0.2328	0.0075	0.0679	0.1605	0.0631	0.2421	9.407	4.439	2.841
5	2.3723	0.5538	-0.7946	0.3743	0.0901	0.4451	-0.0535	0.0117	-0.1525	0.0187	0.0082	-0.256	0.1521	0.1136	0.0453	0.2169	0.0638	0.0428	0.2455	0.0654	0.4098	32.666	-1.328	22.87
6	1.644	-0.6078	-0.1012	1.6863	-0.8547	1.8599	-0.094	-0.401	0.2653	0.2963	-0.0313	-0.3577	-0.108	0.4897	0.1252	0.228	0.0166	-0.1243	0.3944	-0.0015	0.4081	27.767	1.565	47.132
7	1.726	-0.3885	0.1627	0.4974	0.2633	1.2858	0.0633	-0.3667	-0.2222	0.027	0.0006	0.1272	0.2019	-0.0727	-0.064	0.1854	-0.0919	-0.0215	0.1231	0.0524	0.1719	-4.446	-4.626	148.182
8	2.682	1.0466	0.2818	0.9916	0.1175	1.007	0.0595	0.0333	0.377	-0.0256	0.0212	0.3535	-0.0926	-0.2634	-0.0807	0.1657	-0.0107	-0.0255	0.0968	0.0568	0.2707	-19.458	4.829	130.563
9	2.5268	-1.0221	-0.0215	2.2372	-1.2013	1.7546	0.1029	0.8356	0.0043	-0.4294	0.0897	0.2164	0.3592	-0.2434	-0.1926	0.3047	-0.0154	-0.1262	0.4886	0.1062	0.1462	-8.367	5.929	101.488
10	2.6459	0.0482	-0.2785	1.471	0.9561	2.3933	0.0772	0.9496	0.5076	-0.3663	-0.1119	0.013	-0.23	0.1222	0.0347	0.36	0.0986	-0.045	0.4867	0.1971	0.1583	16.139	9.971	98.685
11	1.8331	0.2791	-0.0633	0.8901	0.0077	0.5719	0.0997	0.2841	-0.1022	-0.234	-0.1246	0.01	0.1469	0.0267	0.025	0.2055	0.1036	0.0261	0.0665	0.0565	0.1478	34.905	-0.912	120.976
12	2.3011	-0.3542	-0.4583	1.1945	-0.9771	1.9986	0.0939	-0.4583	0.1897	0.0792	-0.2108	-0.1086	0.0434	0.2122	0.1168	0.139	-0.0325	-0.0474	0.0983	0.0362	0.1393	26.24	-0.875	144.325
13	1.8633	-0.7891	-0.2522	1.4455	1.1292	1.8624	-0.1303	-0.2325	-0.4034	0.1156	0.0904	0.1254	0.2821	0.0436	0.04	0.2324	0.0551	0.0882	0.1623	0.0778	0.2471	73.171	-6.193	101.938
14	2.573	1.3379	0.1835	0.7884	-0.1241	1.6277	0.042	-0.0287	0.0766	0.0364	-0.0324	0.3895	-0.2795	-0.1093	-0.0096	0.2239	0.0338	0.0189	0.1335	-0.0538	0.378	58.44	3.429	84.1
15	2.7084	-0.2773	0.1725	2.3747	-0.8066	1.6646	0.0241	1.1069	-0.3067	-0.3753	-0.0079	0.3418	0.0764	-0.0365	-0.0161	0.3547	-0.0009	-0.1149	0.6816	-0.1797	0.2377	70.051	4.297	55.197
16	3.3605	-0.3053	-0.4104	0.6196	0.8781	1.7989	-0.0126	1.1345	0.1173	-0.3147	0.0165	-0.0329	-0.377	0.3974	-0.0039	0.4762	-0.1115	0.0175	0.8745	-0.0707	0.1394	94.576	8.455	52.802
17	2.8745	0.7505	0.0367	1.3049	-0.2743	1.277	-0.0004	0.376	-0.4011	-0.2283	-0.0565	-0.088	0.0906	0.6092	0.0569	0.2167	0.0459	0.0938	0.6187	-0.1032	0.1644	113.033	-2.185	75.583
18	1.8524	-0.4594	-0.2203	1.5343	-0.4797	1.7548	-0.0931	-0.2525	-0.1694	0.0939	0.0981	-0.0764	-0.0698	0.4681	-0.005	0.1969	0.0139	0.0223	0.396	-0.0184	0.1834	103.981	-1.908	98.729

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	4 - 253	4 - 253
2	X-RAY DIFFRACTION	1	A	LB	3002 - 3047	1 - 46
3	X-RAY DIFFRACTION	1	A	S - TA	2011 - 2012	1
4	X-RAY DIFFRACTION	2	B	B	4 - 253	4 - 253
5	X-RAY DIFFRACTION	2	B	MB	2029 - 2073	7 - 51
6	X-RAY DIFFRACTION	2	B	T - UA	2021 - 2022	1
7	X-RAY DIFFRACTION	3	C	C	4 - 253	4 - 253
8	X-RAY DIFFRACTION	3	C	NB	3010 - 3057	8 - 55
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