PDB-2zae: Crystal structure of protein Ph1601p in complex with protein Ph17...

ID or keywords:

Entry

Database: PDB / ID: 2zae

Title

Crystal structure of protein Ph1601p in complex with protein Ph1771p of archaeal ribonuclease P from Pyrococcus horikoshii OT3

Components

(Ribonuclease P protein component ...) x 2

Keywords

HYDROLASE / Ribonuclease P Protein subunits / hetero dimer / tRNA processing

Function / homology

Function and homology information

ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.21 Å

Authors

Honda, T. / Kakuta, Y. / Kimura, M.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P.
Authors: Honda, T. / Kakuta, Y. / Kimura, K. / Saho, J. / Kimura, M.

History

Deposition	Oct 4, 2007	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 14, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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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Validation report

Summary document	2zae_validation.pdf.gz	491.3 KB	Display	wwPDB validaton report
Full document	2zae_full_validation.pdf.gz	499.6 KB	Display
Data in XML	2zae_validation.xml.gz	20.4 KB	Display
Data in CIF	2zae_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/2zae ftp://data.pdbj.org/pub/pdb/validation_reports/za/2zae	HTTPS FTP

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Related structure data

Related structure data	1v76S 1x0tS S: Starting model for refinement
Similar structure data	4w1u-d 2ki7-d 3skr-2 5tp1-4 4k82-d 2q7t-2 3slq-1 6lm3-d 6rpt-1 2l6f-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) 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	#260 - Aug 2021 Ribonuclease P similarity (10)

Deposited unit

A: Ribonuclease P protein component 1

B: Ribonuclease P protein component 4

C: Ribonuclease P protein component 1

D: Ribonuclease P protein component 4

hetero molecules

60.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribonuclease P protein component 1

B: Ribonuclease P protein component 4

hetero molecules

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

2

C: Ribonuclease P protein component 1

D: Ribonuclease P protein component 4

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.829, 127.070, 51.857
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-150- HOH

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Ribonuclease P protein component ... , 2 types, 4 molecules ACBD

#1: Protein	Ribonuclease P protein component 1 / RNase P component 1 Mass: 15070.599 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: rnp1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: O59425, ribonuclease P
#2: Protein	Ribonuclease P protein component 4 / RNase P component 4 Mass: 14626.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: rnp4 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: O59248, ribonuclease P

#1: Protein

Ribonuclease P protein component 1 / RNase P component 1

Mass: 15070.599 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: rnp1 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: O59425, ribonuclease P

#2: Protein

Ribonuclease P protein component 4 / RNase P component 4

Mass: 14626.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: rnp4 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: O59248, ribonuclease P

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Non-polymers , 4 types, 194 molecules

#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 179 / 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: 40.74 %
Crystal grow	Temperature: 293.4 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M KNO3, 50mM NaCl,50mM Tris-HCl , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: RIGAKU JUPITER 210 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 25221 / Num. obs: 25221 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / R_merge(I) obs: 0.064 / R_sym value: 0.064 / Net I/σ(I): 33.8
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.369 / Mean I/σ(I) obs: 3.15 / Num. unique all: 1552 / R_sym value: 0.369 / % possible all: 89.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X0T, 1V76

1x0t

1v76

Resolution: 2.21→42.64 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.93 / SU B: 11.868 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25005	1273	5 %	RANDOM
R_work	0.19938	-	-	-
obs	0.20191	23939	98.52 %	-

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: 36.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.17 Å²	0 Å²	0 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	0.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.21→42.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3365	0	62	179	3606

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3495
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.397	1.977	4675
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.285	5	406
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.607	20.065	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.928	15	686
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.117	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	503
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2557
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1435
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	2303
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	179
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.229	0.2	79
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.214	0.2	13
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.651	1.5	2113
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.104	2	3292
X-RAY DIFFRACTION	r_scbond_it	1.606	3	1567
X-RAY DIFFRACTION	r_scangle_it	2.46	4.5	1381
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.207→2.264 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.307	73	-
R_work	0.232	1552	-
obs	-	-	87.84 %

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	10.0263	-2.3577	2.6881	5.8309	-2.6618	3.5777	-0.226	-0.2634	0.1831	0.454	0.1246	-0.1865	-0.5492	-0.1321	0.1014	-0.0025	0.0285	-0.033	0.0889	0.0174	0.1042	11.564	-14.6559	-6.7273
2	4.0035	-1.8971	-1.0227	5.69	0.0603	3.8416	-0.1749	0.0799	-0.121	-0.2479	0.0273	-0.1788	0.3974	0.2394	0.1475	0.0732	0.0875	0.0405	0.0674	0.0327	0.1395	26.4866	-25.1646	-12.9144
3	3.9018	2.1607	-4.0033	1.2374	-1.5777	14.1186	0.2729	-0.7457	0.236	0.9049	0.0673	0.0257	-1.5749	0.2935	-0.3403	0.2017	0.0657	-0.023	0.0558	0.023	0.0683	24.5567	-23.035	6.4743
4	8.5608	1.6327	0.0543	4.6256	-1.2755	5.1134	0.0938	-0.2669	0.0408	0.1935	-0.1508	-0.44	-0.3423	0.2405	0.0571	0.038	0.0425	-0.0097	0.0631	0.0117	0.1351	24.4662	-16.2732	-3.8103
5	4.6467	-0.9604	1.0446	2.6344	-2.1941	2.0215	-0.0544	-0.3211	0.0263	0.2517	0.0902	-0.1118	-0.2648	-0.1866	-0.0358	0.0242	0.0317	-0.0596	0.1239	-0.0113	0.1091	22.6566	-17.0743	2.3231
6	4.5425	2.4136	0.0356	10.0203	-2.5732	5.2661	-0.2466	0.1495	0.1275	-0.5657	0.0882	-0.5213	0.171	0.6123	0.1584	0.0023	0.0604	-0.0176	0.0683	0.0228	0.1131	30.7986	-23.7135	-7.1629
7	11.5908	-3.6931	1.9018	5.6876	-1.6978	5.4043	0.0756	0.9701	-0.2196	-0.4859	-0.5331	-0.586	0.3636	1.2038	0.4575	0.061	0.0567	0.0366	0.1664	0.0994	0.0723	30.0963	-21.0431	-21.8751
8	7.4669	-2.2851	-1.5393	3.6688	-2.2431	5.6793	-0.0185	-0.1097	0.2349	-0.0906	-0.0091	-0.0966	-0.2063	0.0222	0.0276	0.0904	0.0127	-0.0229	0.0532	0.0274	0.1212	18.4642	-10.7524	-15.8934
9	16.9633	1.0905	-0.0381	12.0489	-2.6919	5.1174	0.2551	1.3591	0.8056	-0.7107	-0.1805	-0.3802	-0.1218	0.6072	-0.0746	0.1595	0.1108	0.1414	0.1402	0.1329	-0.0066	30.0467	-13.4471	-26.9725
10	1.0518	0.2461	2.204	2.1552	0.8081	4.659	0.3061	-0.0287	-0.0609	0.0438	-0.1432	-0.1543	0.5296	0.0481	-0.163	0.1265	-0.0449	-0.0442	0.056	0.0392	0.0922	15.7195	-7.8418	-25.0865
11	11.1928	-4.9788	1.867	4.3626	1.322	2.4685	0.8045	1.5984	0.194	-1.0178	-0.4667	-0.3111	-0.2583	-0.0008	-0.3378	0.2178	0.0274	0.0367	0.1289	0.0148	0.0771	6.9243	-2.9114	-40.3034
12	9.752	1.0972	-0.0198	4.9238	3.1279	10.1764	0.0253	0.5405	-0.2852	-0.2103	0.0425	0.0047	0.2847	0.125	-0.0678	0.0919	-0.0214	-0.0265	0.0522	0.0263	0.1228	13.0114	-2.0252	-31.6619
13	9.3408	-1.1032	-1.0181	2.4952	2.4069	3.3891	0.2398	0.0333	0.5657	0.2912	-0.4551	-0.0308	-0.6179	0.0067	0.2153	0.0568	0.0303	0.0234	0.1376	0.0142	0.1042	74.1782	-12.3751	-6.0188
14	6.3543	1.9009	2.0939	4.3555	-1.4807	3.7681	-0.1344	0.2812	-0.3026	-0.1397	0.2734	0.1895	0.4501	-0.3286	-0.139	0.1052	-0.095	0.0232	0.1018	0.0037	0.0782	56.8706	-24.921	-4.4423
15	1.5428	0.8924	2.8432	7.7964	0.1313	22.4312	-0.2463	-0.1216	-0.324	0.0183	0.0502	0.0319	0.1222	0.4259	0.1961	0.0414	-0.0976	-0.0119	0.0771	0.0107	0.141	61.6561	-19.9786	-6.1639
16	1.0722	-1.0891	0.4875	2.1562	-0.8403	4.7909	-0.017	0.0724	-0.0159	-0.2097	-0.0075	0.2241	-0.0275	0.0253	0.0245	0.0199	-0.0597	-0.0025	0.0866	0.044	0.1359	60.2965	-12.5657	-14.9795
17	6.3917	0.5166	1.4946	0.1154	-0.532	6.1322	0.0982	0.1125	0.3335	-0.3041	-0.0558	0.0414	0.0437	-0.0467	-0.0424	0.0192	0.0128	-0.0064	0.0925	0.0309	0.1405	61.8014	-11.0026	-14.2827
18	4.0968	-1.718	-0.2342	5.7513	-0.2847	4.7055	-0.0894	-0.0099	0.0526	-0.1308	0.2838	0.3787	0.1054	-0.5238	-0.1945	-0.0203	-0.088	-0.023	0.1463	0.0913	0.1272	53.9479	-19.1696	-8.8371
19	21.1731	11.7007	7.4802	8.5494	7.4994	33.8929	1.039	-1.0026	0.2702	0.999	-0.6682	1.1823	-0.4817	-3.0444	-0.3708	-0.1102	-0.0786	0.1567	0.2753	0.0737	0.1797	47.5665	-25.3785	6.321
20	5.3392	1.5209	-0.1458	1.8488	-0.178	2.6181	0.0233	-0.1207	0.0627	0.1775	0.0135	0.0794	-0.0379	-0.0438	-0.0369	0.0668	0.002	0.0163	0.0997	-0.0018	0.1127	64.961	-15.7985	4.1518
21	27.0896	-14.2574	3.7743	13.6045	-0.7128	9.2899	0.0114	-0.9198	-0.3812	0.4723	0.1535	0.5378	0.1542	-1.1022	-0.1648	0.0452	-0.1036	0.1148	0.08	0.0134	0.0806	55.6677	-18.954	12.6159
22	1.5025	0.1125	-0.1256	4.0475	-0.2209	2.3457	0.2551	-0.1483	0.0344	0.1267	-0.0777	0.0348	0.3163	-0.0321	-0.1775	0.0658	-0.0073	0.0107	0.093	0.0131	0.0985	70.158	-14.1566	14.703
23	2.2173	1.5314	-3.2676	2.5571	-6.0271	14.2962	-0.1192	-0.5605	0.2151	0.2378	0.0308	-0.0835	0.9976	0.9875	0.0883	0.4842	0.0818	0.1071	-0.0133	-0.0064	0.144	73.0956	-21.0936	31.1502
24	6.1087	1.8465	-2.4293	3.6641	-2.6552	4.9437	-0.1704	-0.2338	-0.3479	0.1489	0.2276	-0.0854	0.9146	0.0368	-0.0572	0.2333	0.0064	0.0195	0.0478	-0.0097	0.0531	70.4612	-14.4872	22.842

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	18 - 30	18 - 30
2	X-RAY DIFFRACTION	2	A	A	31 - 52	31 - 52
3	X-RAY DIFFRACTION	3	A	A	53 - 66	53 - 66
4	X-RAY DIFFRACTION	4	A	A	67 - 80	67 - 80
5	X-RAY DIFFRACTION	5	A	A	81 - 93	81 - 93
6	X-RAY DIFFRACTION	6	A	A	94 - 122	94 - 122
7	X-RAY DIFFRACTION	7	B	B	11 - 28	11 - 28
8	X-RAY DIFFRACTION	8	B	B	29 - 51	29 - 51
9	X-RAY DIFFRACTION	9	B	B	52 - 61	52 - 61
10	X-RAY DIFFRACTION	10	B	B	62 - 81	62 - 81
11	X-RAY DIFFRACTION	11	B	B	82 - 92	82 - 92
12	X-RAY DIFFRACTION	12	B	B	93 - 108	93 - 108
13	X-RAY DIFFRACTION	13	C	C	17 - 29	17 - 29
14	X-RAY DIFFRACTION	14	C	C	30 - 46	30 - 46
15	X-RAY DIFFRACTION	15	C	C	47 - 52	47 - 52
16	X-RAY DIFFRACTION	16	C	C	53 - 76	53 - 76
17	X-RAY DIFFRACTION	17	C	C	77 - 95	77 - 95
18	X-RAY DIFFRACTION	18	C	C	96 - 121	96 - 121
19	X-RAY DIFFRACTION	19	D	D	12 - 17	12 - 17
20	X-RAY DIFFRACTION	20	D	D	18 - 51	18 - 51
21	X-RAY DIFFRACTION	21	D	D	52 - 62	52 - 62
22	X-RAY DIFFRACTION	22	D	D	63 - 82	63 - 82
23	X-RAY DIFFRACTION	23	D	D	83 - 92	83 - 92
24	X-RAY DIFFRACTION	24	D	D	93 - 109	93 - 109

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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Ribonuclease P protein component ... , 2 types, 4 molecules ACBD

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Non-polymers , 4 types, 194 molecules

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-Ribonuclease P protein component ... , 2 types, 4 molecules ACBD

-Non-polymers , 4 types, 194 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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This page

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This web site

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Options

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Open data

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

-
Ribonuclease P protein component ... , 2 types, 4 molecules ACBD

-
Non-polymers , 4 types, 194 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi