PDB-3djv: Bovine Seminal Ribonuclease- cytidine 3' phosphate complex

ID or keywords:

Entry

Database: PDB / ID: 3djv

Title

Bovine Seminal Ribonuclease- cytidine 3' 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 /

metabolic process /

nucleic acid binding /

lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding
Similarity search - Function

Biological species

Bos taurus (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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3djv.cif.gz	70 KB	Display	PDBx/mmCIF format
PDB format	pdb3djv.ent.gz	52.4 KB	Display	PDB format
PDBx/mmJSON format	3djv.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/dj/3djv ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3djv	HTTPS FTP

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Related structure data

Related structure data	3djoC 3djpC 3djqC 3djxC 1r5dS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3djo-d 1y92-d 3bco-d 11ba-d 3bcm-d 11bg-d 1r5d-d 3djx-d 3djq-d 1tq9-d 1r5c-d 3f8g-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

27.9 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)	48.355, 58.997, 81.994
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 (cattle) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical	ChemComp-C3P / CYTIDINE-3'-MONOPHOSPHATE / Cytidine monophosphate Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₃O₈P
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.14 Å³/Da / Density % sol: 42.65 %
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→27.6 Å / Num. all: 31120 / Num. obs: 31086 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / B_iso Wilson estimate: 16.4 Å² / R_sym value: 0.036 / Net I/σ(I): 26.2
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 7804 / R_sym value: 0.273 / % possible all: 85.1

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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→27.6 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.943 / SU B: 3.041 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20363	1575	5.1 %	RANDOM
R_work	0.17667	-	-	-
obs	0.17809	29510	97.64 %	-
all	-	31120	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 13.69 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	0 Å²
2-	-	-0.2 Å²	0 Å²
3-	-	-	0.17 Å²

Refine analyze

Luzzati coordinate error obs: 0.197 Å

Refinement step

Cycle: LAST / Resolution: 1.6→27.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1882	0	42	309	2233

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1972
X-RAY DIFFRACTION	r_angle_refined_deg	1.342	1.971	2661
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.542	5	246
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.209	24.865	74
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.618	15	365
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.804	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	295
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1420
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	940
X-RAY DIFFRACTION	r_nbtor_refined	0.289	0.2	1349
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.117	0.2	242
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.15	0.2	62
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.11	0.2	35
X-RAY DIFFRACTION	r_mcbond_it	0.512	1.5	1275
X-RAY DIFFRACTION	r_mcangle_it	0.895	2	2013
X-RAY DIFFRACTION	r_scbond_it	1.485	3	775
X-RAY DIFFRACTION	r_scangle_it	2.394	4.5	648

LS refinement shell

Resolution: 1.597→1.638 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.25	95	-
R_work	0.193	1863	-
obs	-	-	85.61 %

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	5.6273	0.3354	-1.7783	2.2686	0.6301	6.8477	0.1049	-0.4449	-0.0008	0.2967	-0.1246	-0.0855	0.0777	0.3938	0.0197	0.0476	-0.0312	-0.0059	0.0648	0.0011	-0.0067	11.11	19.4628	23.2601
2	6.2776	-2.6229	0.9468	7.4824	-3.8659	3.7598	0.2164	0.4075	0.3185	-0.4804	-0.0999	0.0535	0.1247	0.0244	-0.1165	0.049	0.0052	-0.0019	0.043	0.0031	0.0203	7.0092	22.6078	9.518
3	3.3837	1.0092	-0.0998	1.9527	-0.7547	2.1474	0.03	0.1027	0.0731	-0.1485	0.0244	0.2625	0.0783	-0.1692	-0.0544	0.0033	-0.0068	-0.0055	0.0178	-0.0071	0.0515	18.683	27.345	5.475
4	14.4668	-6.0402	-7.1881	10.2616	12.4493	15.1052	0.1109	-0.9287	0.195	1.0315	-0.0782	0.042	0.1596	-0.1091	-0.0327	0.0789	-0.0166	0.0154	0.1017	-0.0333	-0.035	23.8376	32.0735	16.7223
5	2.6859	0.383	-0.7074	1.2172	0.258	1.2722	0.0264	0.0554	0.0107	-0.0435	-0.0038	-0.0156	-0.0402	-0.0082	-0.0226	0.0572	0.0029	-0.0131	0.0228	-0.0032	0.0452	34.6896	31.4998	1.2953
6	0.7861	0.489	0.1871	5.3067	4.5374	7.4397	0.0745	0.0077	-0.01	-0.2051	0.1082	-0.1759	-0.349	0.0002	-0.1827	0.0618	-0.0209	0.009	0.0063	0.0053	0.033	42.5822	42.747	2.5107
7	9.8052	1.427	-3.5671	3.2679	-0.9192	4.6238	-0.0617	0.4148	0.0155	-0.2731	0.1443	-0.007	0.1936	0.1059	-0.0826	0.0811	0.0025	-0.0285	0.0523	-0.0004	0.0249	31.8979	33.5222	-5.6141
8	4.0505	-0.5556	-1.3197	1.4793	-2.1846	7.8655	0.0903	-0.4232	0.3217	0.3418	0.1454	0.5111	-0.5136	-0.6559	-0.2357	-0.0126	0.0176	0.0737	0.024	-0.0578	0.1142	15.8879	37.958	11.8618
9	4.9414	0.8065	-2.1649	0.6077	-0.711	3.0583	-0.0483	0.2488	0.2371	-0.0961	0.07	0.2147	-0.0243	-0.1181	-0.0217	0.0745	0.0157	-0.0281	0.0088	0.0147	0.0861	24.6469	35.7905	-1.9507
10	4.9204	-3.3742	2.4493	4.5127	-1.6342	3.0221	-0.0682	-0.0475	0.1023	-0.0301	0.0818	-0.0559	-0.0751	-0.0233	-0.0136	0.0449	-0.0165	-0.0112	0.0234	0.0101	0.0387	40.4735	35.6662	4.9837
11	9.327	0.8149	-0.4229	2.3177	-1.1896	4.2501	0.0512	-0.6908	-0.117	0.2733	-0.2179	-0.0975	-0.1143	0.1589	0.1666	0.0323	-0.0186	-0.0154	0.0491	0.024	0.0143	35.9517	28.7526	12.4712
12	1.5402	1.2578	-0.5272	1.0279	-0.4153	0.5174	-0.1273	0.2668	-0.0805	-0.0648	0.1223	0.0314	0.0451	-0.0789	0.005	0.0215	-0.007	0.0074	0.0294	-0.0137	0.0386	23.2385	22.764	1.0792
13	0.9995	0.4295	-0.4725	1.9384	-0.4447	1.7531	0.0877	0.0029	0.0188	-0.1311	0.0061	-0.147	-0.0254	0.0198	-0.0938	-0.0009	-0.0025	0.0085	0.0436	-0.0099	0.0515	18.7707	20.383	11.0035
14	19.2138	-14.5842	0.4881	12.5676	-3.8792	8.2332	-0.1248	-0.6829	-0.0983	0.8532	0.141	-0.9213	-0.0484	0.8757	-0.0162	0.007	0.0187	-0.0921	0.1104	-0.0024	0.0543	22.7732	15.9186	17.8089
15	1.9788	-0.1816	-0.0942	1.2862	-0.3518	1.5018	0.0485	-0.0236	-0.0395	0.0248	-0.0118	0.0467	0.0708	-0.0686	-0.0367	0.0521	0.0008	-0.0055	0.0355	-0.0052	0.04	3.6752	16.2585	14.5137
16	12.0046	-7.5717	8.2453	11.5696	-7.5385	6.4677	0.0141	-0.1005	-0.4137	-0.1784	0.331	0.3862	0.1896	-0.0214	-0.3451	0.0527	-0.0221	-0.0073	0.065	0.0221	-0.0002	0.5204	2.9993	20.843
17	1.2166	0.3997	-0.4557	1.3622	-1.0039	1.7544	0.0214	0.0053	-0.054	-0.0311	0.0463	0.052	0.096	-0.0926	-0.0678	0.0797	-0.0012	-0.0152	0.0454	-0.014	0.0399	3.0019	11.0204	12.9922
18	12.7497	4.6827	13.321	13.0001	9.8273	22.0604	0.1482	0.6364	-0.3206	-0.5301	-0.1998	-1.144	-0.1735	1.7418	0.0515	-0.0663	0.0824	0.0729	0.1218	0.0802	0.116	28.0252	10.1262	9.4733
19	6.423	0.4046	-1.1295	0.2256	-0.1874	1.6737	-0.1265	0.3615	0.0471	-0.0511	0.1009	-0.0786	0.1733	-0.0785	0.0256	0.0973	0.011	0.004	0.0312	-0.0172	0.0564	8.949	12.035	5.0976
20	1.2848	-0.8978	-1.123	2.9186	2.9842	6.5785	0.0596	-0.0474	-0.0712	0.0471	0.0347	-0.0086	0.1123	-0.0282	-0.0943	0.0542	-0.0053	0.0059	0.04	0.0022	0.0148	2.3408	12.6476	20.8883

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 - 11	1 - 11
2	X-RAY DIFFRACTION	2	A	A	12 - 18	12 - 18
3	X-RAY DIFFRACTION	3	A	A	19 - 33	19 - 33
4	X-RAY DIFFRACTION	4	A	A	34 - 39	34 - 39
5	X-RAY DIFFRACTION	5	A	A	40 - 60	40 - 60
6	X-RAY DIFFRACTION	6	A	A	61 - 75	61 - 75
7	X-RAY DIFFRACTION	7	A	A	76 - 83	76 - 83
8	X-RAY DIFFRACTION	8	A	A	84 - 95	84 - 95
9	X-RAY DIFFRACTION	9	A	A	96 - 106	96 - 106
10	X-RAY DIFFRACTION	10	A	A	107 - 124	107 - 124
11	X-RAY DIFFRACTION	11	B	B	1 - 11	1 - 11
12	X-RAY DIFFRACTION	12	B	B	12 - 26	12 - 26
13	X-RAY DIFFRACTION	13	B	B	27 - 33	27 - 33
14	X-RAY DIFFRACTION	14	B	B	34 - 39	34 - 39
15	X-RAY DIFFRACTION	15	B	B	40 - 61	40 - 61
16	X-RAY DIFFRACTION	16	B	B	62 - 68	62 - 68
17	X-RAY DIFFRACTION	17	B	B	69 - 86	69 - 86
18	X-RAY DIFFRACTION	18	B	B	87 - 95	87 - 95
19	X-RAY DIFFRACTION	19	B	B	96 - 106	96 - 106
20	X-RAY DIFFRACTION	20	B	B	107 - 124	107 - 124

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