PDB-3tqm: Structure of an ribosomal subunit interface protein from Coxiella...

ID or keywords:

Entry

Database: PDB / ID: 3tqm

Title

Structure of an ribosomal subunit interface protein from Coxiella burnetii

Components

Ribosome-associated factor Y

Keywords

PROTEIN BINDING / Protein synthesis

Function / homology

Function and homology information

primary metabolic process / negative regulation of translational elongation / ribosomal small subunit binding / ribosome binding / cytosolic small ribosomal subunit
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.45 Å

Authors

Rudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 27, 2016	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tqm.cif.gz	160.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tqm.ent.gz	136.3 KB	Display	PDB format
PDBx/mmJSON format	3tqm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tqm_validation.pdf.gz	455.2 KB	Display	wwPDB validaton report
Full document	3tqm_full_validation.pdf.gz	461.7 KB	Display
Data in XML	3tqm_validation.xml.gz	17.8 KB	Display
Data in CIF	3tqm_validation.cif.gz	24.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqm ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqm	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	4hei-2 2bn3-1 4lpt-6 3eud-4 6dg6-6 4hei-1 4bd4-5 2bn1-1 6qqg-1 1m8n-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribosome-associated factor Y

B: Ribosome-associated factor Y

C: Ribosome-associated factor Y

D: Ribosome-associated factor Y

hetero molecules

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

1

A: Ribosome-associated factor Y

hetero molecules

defined by author&software
11.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ribosome-associated factor Y

hetero molecules

defined by author&software
11.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Ribosome-associated factor Y

hetero molecules

defined by author&software
11.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Ribosome-associated factor Y

hetero molecules

defined by author&software
11.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	35.558, 52.616, 71.295
Angle α, β, γ (deg.)	115.950, 90.020, 102.320
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribosome-associated factor Y Mass: 11225.463 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_0745 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DI6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.59 Å³/Da / Density % sol: 52.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200 mM Ammonium Sulfate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.45→50 Å / Num. all: 16806 / Num. obs: 16605 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.45→2.49 Å / % possible all: 87.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→19.608 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7463 / SU ML: 0.38 / σ(F): 1.97 / Phase error: 31.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2673	796	5.01 %
R_work	0.2354	-	-
obs	0.2371	15883	95.81 %
all	-	16679	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 25.05 Å² / k_sol: 0.366 e/Å³

Displacement parameters

B_iso max: 85.74 Å² / B_iso mean: 31.478 Å² / B_iso min: 7.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.5489 Å²	0.4503 Å²	3.403 Å²
2-	-	4.5671 Å²	-0.6192 Å²
3-	-	-	-0.0182 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→19.608 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2947	0	20	164	3131

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3051
X-RAY DIFFRACTION	f_angle_d	0.604	4099
X-RAY DIFFRACTION	f_chiral_restr	0.042	471
X-RAY DIFFRACTION	f_plane_restr	0.003	513
X-RAY DIFFRACTION	f_dihedral_angle_d	14.474	1197

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.45-2.6031	0.3875	130	0.3437	2431	2561	93
2.6031-2.8035	0.3673	122	0.326	2526	2648	95
2.8035-3.0847	0.3771	121	0.3002	2483	2604	94
3.0847-3.5288	0.2448	135	0.2264	2542	2677	97
3.5288-4.4374	0.2342	148	0.1862	2552	2700	97
4.4374-19.6086	0.2041	140	0.1987	2553	2693	98

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	2.3462	0.4905	1.4269	1.3158	-0.4632	1.5667	0.0622	-0.63	-0.1962	-0.262	0.1275	0.1877	0.2408	0.0006	-0.0649	0.1616	-0.0553	-0.0275	0.1181	-0.0229	0.1447	24.0105	5.6943	7.4498
2	3.2795	0.4481	1.732	1.6335	0.8781	1.368	-0.3832	1.2646	-0.0136	-0.182	0.4105	0.1745	0.0985	0.0605	0.1029	0.1932	0.0085	-0.067	0.2159	-0.0458	0.1217	24.2938	13.0875	-1.447
3	1.5157	-0.096	-0.9041	0.3159	0.0696	0.5419	0.1365	0.2511	0.1763	-0.0711	0.1084	0.0224	-0.0896	-0.1711	-0.144	0.2158	-0.0229	0.0261	0.2957	0.0487	0.1884	29.4485	10.3971	6.8183
4	1.3396	-0.2861	0.2321	0.6681	0.0633	0.4746	0.2114	-0.1143	-0.1914	-0.1263	-0.1246	0.1395	-0.0529	-0.0316	0.0085	0.1307	0.0273	-0.0058	0.1252	-0.0017	0.1081	23.8001	15.8597	11.3386
5	2.1422	-0.575	-0.5464	0.3586	-0.0387	0.2684	0.3023	0.1854	0.4438	-0.1858	-0.082	-0.008	-0.1548	-0.1219	-0.2435	0.1753	-0.0029	-0.0185	0.059	-0.0212	0.1505	32.3036	22.4429	4.3545
6	0.1764	-0.3006	0.4712	1.6903	-1.1668	0.9455	0.2459	-0.1205	0.3555	0.3712	0	0.1048	-0.6687	0.1073	-0.1543	0.2911	0.0561	0.0653	0.1228	0.0772	0.3181	21.5231	2.4648	-8.0996
7	4.4925	0.1262	1.1049	0.9367	-0.0893	0.6699	-0.004	0.7029	0.8793	0.183	-0.0223	-0.0132	-0.0397	0.3717	0.1092	0.1925	-0.0031	0.0026	0.1832	0.0854	0.1858	21.2602	5.429	-19.2584
8	0.8985	-0.5128	-0.6033	0.216	0.5605	0.8358	0.0222	0.1628	-0.348	0.0232	-0.127	0.2234	-0.046	0.0161	0.0088	0.1852	0.0262	-0.0463	0.2122	0.0281	0.2388	21.3971	-4.4349	-11.5518
9	1.0176	0.3307	0.2741	0.5412	0.2684	1.206	-0.3909	0.4684	-0.1367	0.0329	0.3519	0.0951	0.1818	0.1384	0.0203	0.1784	0.0126	0.0454	0.1651	0.0364	0.1384	19.7392	-5.0751	-16.4046
10	2.1195	-0.5631	0.6004	0.6658	-0.2865	0.2262	0.6366	0.6475	0.1642	-0.1933	-0.4585	-0.0862	0.1424	-0.2083	-0.1187	0.2935	0.0622	0.0003	0.2866	-0.0675	0.0929	10.8099	-4.929	-24.202
11	0.9422	-1.1241	-0.723	1.4084	1.166	0.9398	0.3019	0.2525	0.8027	-0.1253	-0.1033	-0.7876	0.4146	0.0187	-0.087	0.0988	0.0162	0.0684	0.2735	0.214	0.0667	29.2103	-0.7168	19.3565
12	2.7449	1.0125	0.6731	2.8726	-2.1196	2.5251	0.199	-0.7468	-0.9628	0.0942	0.0574	-0.2916	0.1917	0.2066	-0.3025	0.3251	0.0639	-0.022	0.1613	0.0998	0.2412	29.0132	-3.4405	30.0642
13	0.8487	0.6618	-0.6615	0.751	-0.0329	0.7565	0.2008	-0.5079	-0.0194	0.3676	-0.3516	-0.5287	-0.3077	0.2718	0.1067	-0.3111	0.002	0.3094	0.2799	0.061	-0.073	26.5346	5.6023	24.1033
14	0.5505	-0.1658	0.2048	0.7343	-0.4822	0.3963	-0.2639	-0.1998	0.4226	0.3549	0.2313	0.1583	-0.264	-0.2218	0.1146	0.1821	0.0451	-0.0237	0.278	-0.0454	-0.0319	26.2414	7.2951	27.2324
15	3.4178	0.4929	-0.3135	0.7573	-0.2683	0.4116	0.5347	-0.5835	0.3452	-0.0446	-0.5252	0.0092	0.0388	-0.0465	-0.1469	0.2319	0.0023	0.0474	0.2328	-0.0767	0.1134	16.935	7.0461	35.1003
16	0.7754	-0.0241	-0.0591	0.4032	-0.6609	5.0501	-0.1047	0.0292	0.0683	-0.0575	0.2372	-0.0027	-0.6908	-0.6696	0.1271	0.1369	0.0034	-0.0075	0.1955	-0.0886	0.1738	16.1197	-3.5809	4.1147
17	5.0076	-1.8679	2.4403	1.4656	-1.0374	1.7783	-0.5478	-1.2943	-0.1929	0.4992	0.5072	0.0046	0.0885	-0.4532	0.1079	0.231	0.0544	0.0598	0.3417	-0.0278	0.2109	20.7565	-11.5841	12.9833
18	2.2037	0.5331	2.6155	1.5242	0.4509	4.8316	0.3153	-0.5716	-0.8509	0.0824	0.1107	-0.0774	0.0746	-0.703	-0.3754	0.0431	0.0131	-0.041	0.0807	-0.022	0.2047	16.1209	-9.9812	-1.8072
19	4.364	0.3005	0.493	1.2575	-0.3459	0.4401	-0.0144	-0.4284	-0.4276	-0.2145	0.009	0.1326	0.2246	-0.0014	0.0567	0.1337	-0.015	0.0293	0.0771	-0.0082	0.1226	19.509	-14.5142	2.1106
20	1.5033	0.5704	0.8498	0.3175	0.1573	0.5038	0.2354	-0.002	-0.3009	0.0903	-0.1883	-0.1006	0.5873	-0.2855	-0.1902	0.1813	0.0739	0.0396	-0.0553	0.0458	0.1438	28.9338	-20.6648	7.1179

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:12)	A	1 - 12
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 13:31)	A	13 - 31
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 32:42)	A	32 - 42
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 43:74)	A	43 - 74
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 75:91)	A	75 - 91
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 1:12)	B	1 - 12
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 13:31)	B	13 - 31
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 32:51)	B	32 - 51
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 52:77)	B	52 - 77
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 78:92)	B	78 - 92
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 1:14)	C	1 - 14
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 15:28)	C	15 - 28
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 29:51)	C	29 - 51
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESID 52:77)	C	52 - 77
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 78:93)	C	78 - 93
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 1:15)	D	1 - 15
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 16:33)	D	16 - 33
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 34:51)	D	34 - 51
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 52:77)	D	52 - 77
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 78:93)	D	78 - 93

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