PDB-2e3u: Crystal structure analysis of Dim2p from Pyrococcus horikoshii OT3

ID or keywords:

Entry

Database: PDB / ID: 2e3u

Title

Crystal structure analysis of Dim2p from Pyrococcus horikoshii OT3

Components

Hypothetical protein PH1566

Keywords

RNA BINDING PROTEIN / pre-ribosomal RNA processing factor

Function / homology

Function and homology information

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Tanokura, M. / Jia, M.Z.

Citation

Journal: Proteins / Year: 2007
Title: Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A
Authors: Jia, M.Z. / Ohtsuka, J. / Lee, W.C. / Nagata, K. / Tanokura, M.

History

Deposition	Nov 29, 2006	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 23, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2e3u.cif.gz	47.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2e3u.ent.gz	34.3 KB	Display	PDB format
PDBx/mmJSON format	2e3u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2e3u_validation.pdf.gz	430.1 KB	Display	wwPDB validaton report
Full document	2e3u_full_validation.pdf.gz	431.8 KB	Display
Data in XML	2e3u_validation.xml.gz	8.4 KB	Display
Data in CIF	2e3u_validation.cif.gz	10.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e3/2e3u ftp://data.pdbj.org/pub/pdb/validation_reports/e3/2e3u	HTTPS FTP

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Related structure data

Related structure data	1tuaS S: Starting model for refinement
Similar structure data	5fwh-d 3ntk-2 1a0o-3 6uxn-3 5u0k-5 3hix-5 1ffs-1 6uxp-1 6uxn-5 2g3v-2 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	#86 - Feb 2007 Exosomes similarity (2)

Deposited unit

A: Hypothetical protein PH1566

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	45.949, 47.450, 95.722
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Hypothetical protein PH1566 / PH-DIM2P Mass: 25189.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: O59282
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.08 Å³/Da / Density % sol: 40.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 9% PEG 3000, 0.1M cacodylate buffer, 0.2M Magnesium Chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 14199 / B_iso Wilson estimate: 34.7 Å²

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TUA

1tua

Resolution: 2.3→47.84 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.908 / SU B: 14.503 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26258	467	4.9 %	RANDOM
R_work	0.22756	-	-	-
obs	0.22926	9135	98.18 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.972 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.26 Å²	0 Å²	0 Å²
2-	-	1.33 Å²	0 Å²
3-	-	-	-3.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1320	0	0	20	1340

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1336
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.984	1793
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.997	5	164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.636	22.364	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.835	15	271
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.369	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	207
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	956
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	609
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	915
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	49
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.177	0.2	28
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.208	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.839	1.5	858
X-RAY DIFFRACTION	r_mcangle_it	1.374	2	1332
X-RAY DIFFRACTION	r_scbond_it	2.223	3	550
X-RAY DIFFRACTION	r_scangle_it	3.574	4.5	461

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	42	-
R_work	0.263	631	-
obs	-	-	95.19 %

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	21.1602	16.2043	1.186	14.2383	0.6711	5.1546	0.1204	-0.4035	0.4743	-0.0498	-0.4328	0.1573	-0.9645	-0.391	0.3124	0.142	0.063	0.0511	0.0747	0.0049	0.0747	15.9735	8.3291	-4.0481
2	3.5893	2.2351	3.3741	5.4381	-1.653	6.6549	-0.2904	-0.0151	-0.1326	0.4399	-0.1863	0.6286	0.5455	-0.9354	0.4767	0.1319	-0.0814	0.1206	0.198	-0.0697	0.0766	8.6899	-6.5575	-8.5528
3	16.0863	12.6489	-0.2778	18.3932	1.9283	6.9505	0.4469	-0.537	-0.7648	0.9086	-0.3225	-0.8246	1.28	0.2832	-0.1244	0.4036	0.0759	-0.033	0.0669	0.0623	-0.0334	19.9516	-10.1559	-2.5647
4	8.8206	-1.4306	-1.425	2.475	-0.996	3.9853	-0.0541	-0.5985	-0.0073	0.343	-0.2883	0.0276	0.4606	0.5096	0.3423	0.1763	0.0381	0.0406	0.1142	0.0204	0.0281	20.7644	-1.8852	-2.6104
5	27.0378	-8.0604	-4.7673	10.9709	6.7819	4.1946	0.3535	-1.0905	-0.3706	0.6786	-0.1851	0.3634	-0.1578	-0.0255	-0.1684	0.1526	-0.0821	0.0631	0.3277	-0.0296	-0.0375	5.8046	-1.4462	-2.7243
6	8.7721	1.4367	-3.1154	1.772	-1.1168	3.5369	0.1101	-0.3931	-0.4	0.3264	-0.2769	-0.2074	-0.0576	0.2336	0.1668	0.204	0.0218	-0.0239	0.1172	0.0296	0.055	24.4585	5.4278	-2.8188
7	3.271	3.8546	1.6858	4.8153	2.247	1.6601	-0.0748	0.1575	0.1712	0.0371	0.0506	0.0144	0.0042	-0.0962	0.0242	0.1378	0.0376	0.0107	0.1195	0.005	0.0903	19.6381	2.7651	-11.3924
8	7.3986	2.239	-0.3766	2.3661	1.2959	5.9289	0.0597	0.0182	-0.1593	0.3235	-0.0651	-0.0919	0.5201	0.0079	0.0054	0.1668	0.0097	-0.0098	0.0326	-0.0039	0.0718	19.0176	-6.3882	-16.0548
9	9.4645	0.1898	2.512	0.7083	1.6161	4.1464	0.0594	0.2766	0.0915	0.0497	-0.1633	-0.0093	-0.5128	-0.0058	0.1039	0.141	0.0057	-0.0161	0.0807	0.0123	0.0646	17.1925	2.3173	-21.83
10	0.0887	-0.0601	0.1885	0.0412	-0.2002	12.8682	0.52	-0.3478	0.7974	-1.5928	-1.2476	0.629	-0.7731	-2.4025	0.7276	-0.0993	0.1077	-0.2162	0.5704	-0.1119	0.394	1.0877	-1.9371	-30.3512
11	18.8525	-12.4305	-3.5166	12.768	5.7382	3.4923	0.088	0.0107	-0.5054	-0.0707	-0.2441	0.9878	0.5332	-0.5082	0.1561	0.0845	-0.1039	-0.001	0.1646	-0.021	0.075	7.3262	-11.3069	-31.8756
12	10.2711	10.3474	3.4557	10.9254	4.3432	2.6447	0.1707	-0.1645	-0.1005	0.3028	-0.1385	-0.2408	0.0766	-0.0355	-0.0323	0.1859	0.0294	-0.028	0.0856	-0.0102	0.0497	17.4281	-11.2522	-32.0259
13	0.9244	-0.4114	-0.7894	0.9722	-0.6359	6.685	-0.0476	-0.0431	0.0403	-0.2568	-0.1255	0.0302	-0.1555	-0.3401	0.1731	0.1222	-0.0016	-0.0118	0.1026	-0.0239	0.0678	16.4558	-2.5914	-25.4277
14	8.6064	0.9895	8.4016	3.6996	1.8703	8.4298	-0.5404	0.0575	0.6813	-0.1995	0.1155	0.09	-0.8989	-0.2215	0.4249	0.1997	0.0312	-0.0157	0.1262	0.017	0.0541	15.4337	1.4857	-33.0392
15	12.8041	5.6067	12.5815	2.4596	5.7467	24.67	-0.3523	-0.1059	0.4211	-0.4102	-0.5423	-0.0218	-0.6188	-1.8605	0.8946	0.165	0.0908	-0.1128	0.1576	0.0864	0.011	8.7266	-3.7655	-39.9491
16	13.95	-1.6802	10.2028	9.5326	1.4661	9.2173	0.2544	0.8012	-0.0068	-0.6537	-0.0957	0.1398	-0.1419	1.0241	-0.1586	0.1184	0.0007	-0.0007	0.215	0.0803	-0.0271	19.3406	-3.4152	-41.3616

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	33 - 38	33 - 38
2	X-RAY DIFFRACTION	2	A	A	39 - 49	39 - 49
3	X-RAY DIFFRACTION	3	A	A	50 - 60	50 - 60
4	X-RAY DIFFRACTION	4	A	A	61 - 70	61 - 70
5	X-RAY DIFFRACTION	5	A	A	71 - 76	71 - 76
6	X-RAY DIFFRACTION	6	A	A	77 - 88	77 - 88
7	X-RAY DIFFRACTION	7	A	A	89 - 99	89 - 99
8	X-RAY DIFFRACTION	8	A	A	100 - 113	100 - 113
9	X-RAY DIFFRACTION	9	A	A	114 - 125	114 - 125
10	X-RAY DIFFRACTION	10	A	A	126 - 138	126 - 138
11	X-RAY DIFFRACTION	11	A	A	139 - 148	139 - 148
12	X-RAY DIFFRACTION	12	A	A	149 - 156	149 - 156
13	X-RAY DIFFRACTION	13	A	A	157 - 177	157 - 177
14	X-RAY DIFFRACTION	14	A	A	178 - 187	178 - 187
15	X-RAY DIFFRACTION	15	A	A	188 - 195	188 - 195
16	X-RAY DIFFRACTION	16	A	A	196 - 204	196 - 204

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