PDB-3djo: Bovine Seminal Ribonuclease uridine 2' phosphate complex

ID or keywords:

Entry

Database: PDB / ID: 3djo

Title

Bovine Seminal Ribonuclease uridine 2' phosphate complex

Components

Seminal ribonuclease

Keywords

HYDROLASE / Ribonuclease / Allosteric enzyme / Endonuclease / Nuclease / Secreted

Function / homology

Function and homology information

pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region / identical protein binding
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.6 Å

Authors

Dossi, K. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.

Citation

Journal: Eur.J.Med.Chem. / Year: 2009
Title: Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors
Authors: Dossi, K. / Tsirkone, V.G. / Hayes, J.M. / Matousek, J. / Pouckova, P. / Soucek, J. / Zadinova, M. / Zographos, S.E. / Leonidas, D.D.

History

Deposition	Jun 24, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 30, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3djo.cif.gz	71.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3djo.ent.gz	53.7 KB	Display	PDB format
PDBx/mmJSON format	3djo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3djo_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3djo_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3djo_validation.xml.gz	15.8 KB	Display
Data in CIF	3djo_validation.cif.gz	23.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dj/3djo ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3djo	HTTPS FTP

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Related structure data

Related structure data	3djpC 3djqC 3djvC 3djxC 1r5dS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1r5c-d 3djv-d 11ba-d 3bcm-d 3djq-d 1y92-d 3djx-d 3bco-d 1tq9-d 1bsr-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	#105 - Sep 2008 Ribonuclease A similarity (8) #143 - Nov 2011 Toll-like Receptors similarity (8)

Deposited unit

A: Seminal ribonuclease

B: Seminal ribonuclease

hetero molecules

28 kDa, 2 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)	48.311, 59.067, 82.495
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Seminal ribonuclease / Seminal RNase / S-RNase / Ribonuclease BS-1 Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical	ChemComp-U2P / PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER / URIDINE-2'-PHOSPHATE / 2'-URIDINEMONOPHOSPHATE Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₉P
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.02 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2007
Radiation	Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8088 Å / Relative weight: 1
Reflection	Resolution: 1.6→27.7 Å / Num. all: 31871 / Num. obs: 31815 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / B_iso Wilson estimate: 15.6 Å² / R_sym value: 0.066 / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 9056 / R_sym value: 0.466 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
REFMAC	5.3.0037	refinement
MAR345		data collection
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5D

1r5d

Resolution: 1.6→27.7 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.937 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22638	1605	5 %	RANDOM
R_work	0.18414	-	-	-
obs	0.18628	30202	99.83 %	-

Solvent computation

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

Refine analyze

Luzzati coordinate error obs: 0.206 Å

Refinement step

Cycle: LAST / Resolution: 1.6→27.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1882	0	50	327	2259

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1978
X-RAY DIFFRACTION	r_angle_refined_deg	1.171	1.978	2667
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.517	5	246
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.296	24.865	74
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.936	15	365
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.447	15	8
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1428
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	991
X-RAY DIFFRACTION	r_nbtor_refined	0.291	0.2	1359
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	263
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.168	0.2	53
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.137	0.2	44

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	114	-
R_work	0.229	2161	-
obs	-	-	98.4 %

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	6.7081	-0.1307	-1.113	3.1265	2.6762	12.7358	0.0871	-0.4358	0.123	0.3413	-0.0743	-0.1358	0.0615	0.4535	-0.0128	0.0442	-0.025	-0.004	0.0404	-0.0002	-0.002	10.348	19.9404	24.6128
2	1.6362	-0.1106	0.9097	3.827	-3.1014	5.6051	0.0281	0.0096	0.1013	-0.1964	-0.125	-0.108	0.0334	0.1881	0.0969	0.0264	-0.0042	0.0072	0.0393	0.0043	0.0285	9.8336	20.6782	14.7305
3	6.4465	-1.0189	4.0615	2.3833	-3.7912	7.0218	0.5459	0.5591	-0.0831	0.0375	0.0843	0.2922	0.5105	-0.7	-0.6302	0.0255	0.0141	-0.003	0.1039	0.017	0.0746	10.6988	25.9045	1.047
4	1.3869	0.7599	0.2989	2.4264	-1.3905	3.5607	0.0269	-0.0975	-0.05	-0.0194	-0.055	0.1971	-0.0108	-0.0335	0.0281	-0.0053	-0.0013	0.002	0.0243	0.0035	0.0521	21.0128	27.8356	7.247
5	12.1027	-4.6938	-2.2313	3.5229	2.8161	2.6464	0.0086	-1.0577	0.0361	0.5882	0.1084	-0.159	-0.1552	-0.049	-0.117	0.0738	-0.0251	0.0103	0.1418	0.0224	-0.0305	23.6133	32.1734	16.6379
6	3.1847	0.0864	-0.6928	0.7019	-0.135	1.0201	0.1296	0.0352	-0.1794	0.0138	-0.0935	-0.0178	-0.0382	0.0048	-0.0361	0.032	0.0104	-0.0161	0.0149	-0.0081	0.0522	34.2464	31.4354	1.8107
7	2.1124	-2.5756	-1.8022	7.417	5.0652	6.498	0.1566	0.0324	-0.0082	-0.261	-0.0167	-0.1188	-0.417	-0.0411	-0.1399	0.0466	-0.0186	0.0169	-0.0025	0.0014	0.0052	42.2868	43.8107	2.6759
8	3.584	0.7452	-0.0411	1.43	0.2012	0.9017	0.113	0.2361	-0.0232	-0.039	-0.0453	-0.0204	-0.0428	0.0257	-0.0677	0.0564	0.0171	-0.0089	0.0241	0.0134	0.0311	33.9524	36.831	-1.0823
9	6.6546	2.5084	-3.6268	7.9976	-13.524	22.9337	0.1146	-0.4838	0.2698	0.5619	0.3808	0.8226	-0.9657	-0.8758	-0.4954	0.0213	0.0707	0.0867	0.049	-0.0366	0.0373	13.6733	37.8512	14.2641
10	5.4566	0.8431	-3.1312	1.1193	-0.5601	5.268	-0.0481	0.2605	0.0831	-0.0642	0.0743	0.1432	0.173	-0.2133	-0.0262	0.0547	0.0211	-0.0195	0.0065	0.0109	0.0565	23.297	35.6201	-1.0898
11	3.8082	-2.2473	3.5218	3.3248	-2.6047	6.4102	-0.1164	0.2066	0.0346	0.0876	0.0163	-0.2189	-0.1149	0.2151	0.1	0.0396	-0.0072	-0.0129	0.039	0.0047	0.0545	42.8312	35.3473	4.8154
12	6.2026	-4.3508	3.2041	4.5756	-2.4878	3.1768	0.0548	-0.0995	0.0239	-0.1262	0.0281	-0.0115	-0.0469	-0.1055	-0.083	0.0381	-0.0172	-0.0141	0.0099	0.0106	0.0265	38.6133	36.225	4.3311
13	6.3801	0.7649	1.5499	2.1408	0.3186	1.9327	0.0368	-0.3953	-0.0731	0.2027	-0.1223	-0.0979	-0.0354	0.0075	0.0854	0.0145	-0.0253	-0.0156	0.0354	0.0217	0.0305	34.9026	28.7803	10.54
14	6.4256	1.9764	-1.4644	7.8552	3.841	2.8749	-0.4637	0.9345	-0.0196	-0.1616	0.2135	0.4426	-0.0231	-0.3814	0.2502	0.0011	-0.0421	0.0158	0.0368	0.0371	0.0342	22.3415	22.1654	-2.0687
15	4.8011	2.6771	-0.8305	1.7636	-0.8495	8.1189	-0.105	-0.0747	0.1192	-0.2584	0.0694	-0.1569	0.0845	0.1961	0.0356	0.0307	0.0055	0.0499	-0.0108	0.0191	0.05	18.3665	19.0057	7.147
16	3.594	1.1696	-2.0424	6.8093	-0.9693	1.609	0.1571	-0.2697	-0.0826	0.2437	-0.1659	-0.1659	-0.0477	0.238	0.0088	0.0064	-0.0083	-0.0051	0.0588	0.03	0.0226	18.7622	20.6713	15.6227
17	17.2157	5.0733	-4.3993	9.5687	-0.9877	7.4391	0.2716	-1.7705	-0.3405	0.5527	-0.3088	-0.9443	-0.0425	1.0318	0.0372	-0.0558	0.0186	-0.0144	0.1721	0.0667	0.0812	22.9504	12.9144	17.2418
18	2.0186	0.0287	-0.1512	2.1066	-0.9552	1.6667	-0.0193	-0.0293	-0.0259	-0.0191	0.0576	0.0964	0.0395	-0.1799	-0.0383	0.0313	0.0043	-0.0081	0.0413	0.0055	0.0113	2.0345	17.0256	14.5976
19	12.9111	-8.035	8.8923	9.7058	-5.839	6.1441	0.2493	-0.1148	-0.2954	-0.2593	0.2701	0.4503	0.3546	-0.1365	-0.5194	0.0295	-0.0186	-0.0072	0.0868	0.046	-0.0024	0.3884	3.2755	21.0796
20	0.9387	-0.6571	1.8651	7.8534	-7.8037	13.1519	0.0084	0.0497	-0.0708	-0.0252	0.325	0.371	0.0287	-0.3902	-0.3335	-0.0079	-0.0181	-0.0008	0.0594	0.023	0	-3.005	9.3785	19.224
21	8.6698	-0.2343	-0.456	3.1432	0.679	2.294	-0.2547	0.1278	0.1297	-0.2004	0.2388	0.027	0.3582	-0.1464	0.0159	0.096	-0.0224	-0.0119	0.0237	0.0046	-0.0073	4.0024	15.4325	6.6348
22	1.7351	0.6636	2.1434	3.38	-0.2824	7.01	0.0823	0.1544	-0.2879	-0.2072	-0.1738	-0.8514	0.2532	1.0235	0.0915	-0.0189	0.0735	0.082	0.0526	0.0751	0.1456	24.7864	9.5087	9.3399
23	8.0739	0.0789	-0.7375	0.2263	-0.6972	2.1783	-0.1574	0.4669	-0.0678	-0.2519	0.072	-0.0932	0.3496	-0.1435	0.0855	0.1131	-0.012	0.036	-0.0296	-0.0092	0.0197	7.9182	12.1489	5.2143
24	1.047	-0.9189	-1.7909	7.4468	5.9806	10.5239	0.0423	-0.0554	-0.0335	0.02	0.0548	-0.06	0.1525	-0.2208	-0.0971	0.0323	-0.01	-0.0011	0.0458	0.0078	0.0044	2.1668	12.9527	21.0459

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	1 - 9	1 - 9
2	X-RAY DIFFRACTION	2	A	A	10 - 16	10 - 16
3	X-RAY DIFFRACTION	3	A	A	17 - 23	17 - 23
4	X-RAY DIFFRACTION	4	A	A	24 - 33	24 - 33
5	X-RAY DIFFRACTION	5	A	A	34 - 39	34 - 39
6	X-RAY DIFFRACTION	6	A	A	40 - 59	40 - 59
7	X-RAY DIFFRACTION	7	A	A	60 - 69	60 - 69
8	X-RAY DIFFRACTION	8	A	A	70 - 86	70 - 86
9	X-RAY DIFFRACTION	9	A	A	87 - 94	87 - 94
10	X-RAY DIFFRACTION	10	A	A	95 - 105	95 - 105
11	X-RAY DIFFRACTION	11	A	A	106 - 113	106 - 113
12	X-RAY DIFFRACTION	12	A	A	114 - 124	114 - 124
13	X-RAY DIFFRACTION	13	B	B	1 - 14	1 - 14
14	X-RAY DIFFRACTION	14	B	B	15 - 23	15 - 23
15	X-RAY DIFFRACTION	15	B	B	24 - 30	24 - 30
16	X-RAY DIFFRACTION	16	B	B	31 - 35	31 - 35
17	X-RAY DIFFRACTION	17	B	B	36 - 41	36 - 41
18	X-RAY DIFFRACTION	18	B	B	42 - 61	42 - 61
19	X-RAY DIFFRACTION	19	B	B	62 - 68	62 - 68
20	X-RAY DIFFRACTION	20	B	B	69 - 77	69 - 77
21	X-RAY DIFFRACTION	21	B	B	78 - 83	78 - 83
22	X-RAY DIFFRACTION	22	B	B	84 - 96	84 - 96
23	X-RAY DIFFRACTION	23	B	B	97 - 106	97 - 106
24	X-RAY DIFFRACTION	24	B	B	107 - 124	107 - 124

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