PDB-8ssg: Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter...

ID or keywords:

Entry

Database: PDB / ID: 8ssg

Title

Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter thermophilus

Components

RNA-free ribonuclease P

Keywords

HYDROLASE / RNA-free ribonuclease P / Nuclease

Function / homology

RNA-free ribonuclease P / PINc domain ribonuclease / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / PIN-like domain superfamily / RNA-free ribonuclease P

Function and homology information

Biological species

Hydrogenobacter thermophilus TK-6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Mendoza, J. / Wilhelm, C.A. / Mallik, L. / Koutmos, M.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P.
Authors: Wilhelm, C.A. / Mallik, L. / Kelly, A.L. / Brotzman, S. / Mendoza, J. / Anders, A.G. / Leskaj, S. / Castillo, C. / Ruotolo, B.T. / Cianfrocco, M.A. / Koutmos, M.

History

Deposition	May 8, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ssg.cif.gz	268.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8ssg.ent.gz	211.1 KB	Display	PDB format
PDBx/mmJSON format	8ssg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8ssg_validation.pdf.gz	482.1 KB	Display	wwPDB validaton report
Full document	8ssg_full_validation.pdf.gz	522.2 KB	Display
Data in XML	8ssg_validation.xml.gz	47.8 KB	Display
Data in CIF	8ssg_validation.cif.gz	63.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/8ssg ftp://data.pdbj.org/pub/pdb/validation_reports/ss/8ssg	HTTPS FTP

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Related structure data

Related structure data	8ssfC 7f3eS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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 (1) #3 - Mar 2000 DNA Polymerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: RNA-free ribonuclease P

B: RNA-free ribonuclease P

C: RNA-free ribonuclease P

D: RNA-free ribonuclease P

E: RNA-free ribonuclease P

F: RNA-free ribonuclease P

G: RNA-free ribonuclease P

157 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA-free ribonuclease P

B: RNA-free ribonuclease P

C: RNA-free ribonuclease P

D: RNA-free ribonuclease P

E: RNA-free ribonuclease P

F: RNA-free ribonuclease P

G: RNA-free ribonuclease P

A: RNA-free ribonuclease P

B: RNA-free ribonuclease P

C: RNA-free ribonuclease P

D: RNA-free ribonuclease P

E: RNA-free ribonuclease P

F: RNA-free ribonuclease P

G: RNA-free ribonuclease P

defined by author&software
Evidence: gel filtration, mass spectrometry
315 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.317, 113.764, 155.306
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁22₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	1 - 190	1 - 190
2	1	1	THR	THR	1 - 190	1 - 190
3	2	2	THR	THR	1 - 190	1 - 190
4	2	2	THR	THR	1 - 190	1 - 190
5	3	3	THR	THR	1 - 190	1 - 190
6	3	3	THR	THR	1 - 190	1 - 190
7	4	4	THR	THR	1 - 190	1 - 190
8	4	4	THR	THR	1 - 190	1 - 190
9	5	5	LEU	LEU	1 - 189	1 - 189
10	5	5	LEU	LEU	1 - 189	1 - 189
11	6	6	THR	THR	1 - 190	1 - 190
12	6	6	THR	THR	1 - 190	1 - 190
13	7	7	THR	THR	1 - 190	1 - 190
14	7	7	THR	THR	1 - 190	1 - 190
15	8	8	THR	THR	1 - 190	1 - 190
16	8	8	THR	THR	1 - 190	1 - 190
17	9	9	THR	THR	1 - 190	1 - 190
18	9	9	THR	THR	1 - 190	1 - 190
19	10	10	LEU	LEU	1 - 189	1 - 189
20	10	10	LEU	LEU	1 - 189	1 - 189
21	11	11	THR	THR	1 - 190	1 - 190
22	11	11	THR	THR	1 - 190	1 - 190
23	12	12	THR	THR	1 - 190	1 - 190
24	12	12	THR	THR	1 - 190	1 - 190
25	13	13	THR	THR	1 - 190	1 - 190
26	13	13	THR	THR	1 - 190	1 - 190
27	14	14	LEU	LEU	1 - 189	1 - 189
28	14	14	LEU	LEU	1 - 189	1 - 189
29	15	15	THR	THR	1 - 190	1 - 190
30	15	15	THR	THR	1 - 190	1 - 190
31	16	16	THR	THR	1 - 190	1 - 190
32	16	16	THR	THR	1 - 190	1 - 190
33	17	17	LEU	LEU	1 - 189	1 - 189
34	17	17	LEU	LEU	1 - 189	1 - 189
35	18	18	THR	THR	1 - 190	1 - 190
36	18	18	THR	THR	1 - 190	1 - 190
37	19	19	LEU	LEU	1 - 189	1 - 189
38	19	19	LEU	LEU	1 - 189	1 - 189
39	20	20	THR	THR	1 - 190	1 - 190
40	20	20	THR	THR	1 - 190	1 - 190
41	21	21	LEU	LEU	1 - 189	1 - 189
42	21	21	LEU	LEU	1 - 189	1 - 189

NCS ensembles :

ID	Details
1	Global NCS restraints between domains: 1 2
2	Global NCS restraints between domains: 3 4
3	Global NCS restraints between domains: 5 6
4	Global NCS restraints between domains: 7 8
5	Global NCS restraints between domains: 9 10
6	Global NCS restraints between domains: 11 12
7	Global NCS restraints between domains: 13 14
8	Global NCS restraints between domains: 15 16
9	Global NCS restraints between domains: 17 18
10	Global NCS restraints between domains: 19 20
11	Global NCS restraints between domains: 21 22
12	Global NCS restraints between domains: 23 24
13	Global NCS restraints between domains: 25 26
14	Global NCS restraints between domains: 27 28
15	Global NCS restraints between domains: 29 30
16	Global NCS restraints between domains: 31 32
17	Global NCS restraints between domains: 33 34
18	Global NCS restraints between domains: 35 36
19	Global NCS restraints between domains: 37 38
20	Global NCS restraints between domains: 39 40
21	Global NCS restraints between domains: 41 42

#1: Protein	RNA-free ribonuclease P / RNA-free RNase P / Protein-only RNase P Mass: 22482.750 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydrogenobacter thermophilus TK-6 (bacteria) Gene: HTH_1307 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DIV8, ribonuclease P
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.88 Å³/Da / Density % sol: 57.17 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1.0 M Sodium Malonate, pH 5.0, 0.1 M Sodium Acetate trihydrate, pH 4.5, 2% (w/v) polyethylene glycol 20,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2020
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03317 Å / Relative weight: 1
Reflection	Resolution: 3.2→29.84 Å / Num. obs: 30570 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.071 / R_rim(I) all: 0.137 / Net I/σ(I): 12.1
Reflection shell	Resolution: 3.2→3.37 Å / Redundancy: 7.2 % / R_merge(I) obs: 1.799 / Num. unique obs: 4394 / CC_1/2: 0.43 / R_pim(I) all: 1.082 / R_rim(I) all: 2.104

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
Aimless		data scaling
PHASER		phasing
DIALS		data processing
DIALS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7f3e

7f3e

Resolution: 3.2→29.739 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.237 / WR_factor R_work: 0.187 / SU B: 26.21 / SU ML: 0.42 / Average fsc free: 0.9474 / Average fsc work: 0.9639 / Cross valid method: FREE R-VALUE / ESU R Free: 0.479
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2485	1524	4.991 %
R_work	0.1977	29011	-
all	0.2	-	-
obs	-	30535	99.81 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 120.427 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.565 Å²	0 Å²	0 Å²
2-	-	2.988 Å²	0 Å²
3-	-	-	-0.423 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→29.739 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10010	0	0	30	10040

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	10337
X-RAY DIFFRACTION	r_angle_refined_deg	2.076	1.642	13980
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.761	5	1221
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.126	5	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.443	10	1858
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.617	10	523
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	1539
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7734
X-RAY DIFFRACTION	r_nbd_refined	0.24	0.2	4278
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	7112
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	127
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.385	0.2	165
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.418	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	11.399	11.296	4899
X-RAY DIFFRACTION	r_mcangle_it	17.283	20.268	6112
X-RAY DIFFRACTION	r_scbond_it	13.845	12.43	5438
X-RAY DIFFRACTION	r_scangle_it	21.133	22.26	7867
X-RAY DIFFRACTION	r_lrange_it	27.129	141.001	42291

Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight B_iso : 1.22473 / Weight position: 0.12247

Ens-ID	Dom-ID	Rms dev B_iso (Å²)	Rms dev position (Å)
1	1	10.95822	0.34122
1	2	10.95822	0.34122
2	3	13.67154	0.34916
2	4	13.67154	0.34916
3	5	12.88279	0.3042
3	6	12.88279	0.3042
4	7	17.3273	0.29238
4	8	17.3273	0.29238
5	9	13.63768	0.3277
5	10	13.63768	0.3277
6	11	17.8465	0.32311
6	12	17.8465	0.32311
7	13	13.71123	0.33725
7	14	13.71123	0.33725
8	15	13.14204	0.30727
8	16	13.14204	0.30727
9	17	18.21043	0.56052
9	18	18.21043	0.56052
10	19	13.98162	0.52818
10	20	13.98162	0.52818
11	21	18.7327	0.46269
11	22	18.7327	0.46269
12	23	14.38642	0.31856
12	24	14.38642	0.31856
13	25	15.94415	0.39887
13	26	15.94415	0.39887
14	27	13.5128	0.40712
14	28	13.5128	0.40712
15	29	16.30374	0.44679
15	30	16.30374	0.44679
16	31	18.41926	0.29683
16	32	18.41926	0.29683
17	33	15.21738	0.3012
17	34	15.21738	0.3012
18	35	20.01345	0.32021
18	36	20.01345	0.32021
19	37	12.30866	0.30147
19	38	12.30866	0.30147
20	39	12.53832	0.29575
20	40	12.53832	0.29575
21	41	13.92311	0.33239
21	42	13.92311	0.33239

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.2-3.282	0.353	109	0.346	2065	0.346	2174	0.87	0.903	100	0.347
3.282-3.371	0.355	102	0.316	2053	0.318	2155	0.901	0.92	100	0.316
3.371-3.467	0.285	95	0.282	2001	0.282	2096	0.939	0.941	100	0.272
3.467-3.573	0.288	100	0.231	1934	0.234	2034	0.95	0.962	100	0.217
3.573-3.688	0.3	104	0.221	1855	0.225	1959	0.944	0.966	100	0.207
3.688-3.815	0.279	87	0.209	1844	0.212	1931	0.95	0.971	100	0.189
3.815-3.957	0.295	77	0.204	1774	0.207	1851	0.936	0.973	100	0.184
3.957-4.115	0.226	78	0.188	1692	0.19	1770	0.963	0.976	100	0.167
4.115-4.295	0.22	81	0.163	1631	0.166	1713	0.967	0.983	99.9416	0.147
4.295-4.5	0.258	80	0.17	1570	0.174	1651	0.959	0.982	99.9394	0.15
4.5-4.737	0.18	83	0.16	1486	0.161	1569	0.977	0.985	100	0.145
4.737-5.016	0.26	74	0.171	1423	0.176	1497	0.958	0.981	100	0.157
5.016-5.352	0.206	81	0.179	1325	0.18	1406	0.973	0.98	100	0.164
5.352-5.765	0.229	71	0.159	1245	0.163	1316	0.974	0.984	100	0.143
5.765-6.292	0.264	70	0.2	1152	0.203	1222	0.953	0.976	100	0.18
6.292-6.995	0.287	65	0.214	1062	0.218	1127	0.949	0.973	100	0.196
6.995-8.004	0.238	52	0.187	953	0.189	1006	0.971	0.978	99.9006	0.182
8.004-9.63	0.22	41	0.163	830	0.165	871	0.976	0.983	100	0.17
9.63-12.957	0.221	44	0.171	671	0.174	715	0.971	0.982	100	0.195
12.957-29.739	0.269	30	0.304	445	0.301	476	0.939	0.932	99.7899	0.333

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