PDB-5vxb: Crystal structure of Caulobacter crescentus ProXp-ala at 1.69 Angstrom

ID or keywords:

Entry

Database: PDB / ID: 5vxb

Title

Crystal structure of Caulobacter crescentus ProXp-ala at 1.69 Angstrom

Components

ProXp-ala

Keywords

RNA BINDING PROTEIN / tRNA trans-editing domain

Function / homology

Function and homology information

aminoacyl-tRNA editing activity /

Biological species

Caulobacter crescentus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 Å

Authors

Foster, M.P. / Musier-Forsyth, K. / Nakanishi, K. / Ma, X.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM113656	United States
Department of Energy (DOE, United States)	GUP-51294	United States

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Conformational and chemical selection by a trans-acting editing domain.
Authors: Danhart, E.M. / Bakhtina, M. / Cantara, W.A. / Kuzmishin, A.B. / Ma, X. / Sanford, B.L. / Kosutic, M. / Goto, Y. / Suga, H. / Nakanishi, K. / Micura, R. / Foster, M.P. / Musier-Forsyth, K.

History

Deposition	May 23, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 16, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Aug 23, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 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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Download

PDBx/mmCIF format	5vxb.cif.gz	208.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5vxb.ent.gz	169.4 KB	Display	PDB format
PDBx/mmJSON format	5vxb.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/vx/5vxb ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vxb	HTTPS FTP

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Related structure data

Related structure data	1vjfS S: Starting model for refinement
Similar structure data	1juq-1 4ynl-1 2z93-1 5h5r-d 6zcn-2 6zda-2 3ulh-1 6zcm-1 5fjq-2 1vjf-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) 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

1vjfS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ProXp-ala

B: ProXp-ala

C: ProXp-ala

55.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ProXp-ala

defined by author
Evidence: gel filtration
18.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ProXp-ala

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

3

C: ProXp-ala

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

4

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	62.042, 67.733, 62.927
Angle α, β, γ (deg.)	90.00, 118.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ProXp-ala Mass: 18570.400 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter crescentus (strain ATCC 19089 / CB15) (bacteria) Strain: ATCC 19089 / CB15 / Gene: CC_0111 / Production host: Escherichia coli (E. coli) Strain (production host): BL-21-CodonPlus(DE3)-RIL (Agilent) References: UniProt: Q9ABV9
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ProXp-ala

Mass: 18570.400 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Caulobacter crescentus (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: CC_0111 / Production host:

Escherichia coli (E. coli)
Strain (production host): BL-21-CodonPlus(DE3)-RIL (Agilent)
References: UniProt: Q9ABV9

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 424 / 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: 40.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.005M Trisodium Citrate(pH5.6), 15% Glycerol, 25.5% w/v PEG4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.69→19.88 Å / Num. obs: 51097 / % possible obs: 99.6 % / Redundancy: 6.7 % / R_pim(I) all: 0.026 / Net I/σ(I): 16.3
Reflection shell	Resolution: 1.69→1.78 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 7401 / R_pim(I) all: 0.228 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS	NA	data reduction
XDS	NA	data scaling
PHASER	NA	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VJF

1vjf

Resolution: 1.69→19.805 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1896	2047	4.01 %
R_work	0.1664	-	-
obs	0.1673	51071	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.69→19.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3812	0	0	424	4236

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3911
X-RAY DIFFRACTION	f_angle_d	0.792	5302
X-RAY DIFFRACTION	f_dihedral_angle_d	14.834	2329
X-RAY DIFFRACTION	f_chiral_restr	0.05	614
X-RAY DIFFRACTION	f_plane_restr	0.005	688

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.69-1.7293	0.2502	130	0.2445	3202	X-RAY DIFFRACTION	98
1.7293-1.7725	0.243	136	0.2302	3259	X-RAY DIFFRACTION	100
1.7725-1.8204	0.2444	136	0.2132	3283	X-RAY DIFFRACTION	100
1.8204-1.8739	0.2369	144	0.199	3245	X-RAY DIFFRACTION	100
1.8739-1.9344	0.2209	134	0.1866	3267	X-RAY DIFFRACTION	100
1.9344-2.0035	0.2445	125	0.1694	3266	X-RAY DIFFRACTION	100
2.0035-2.0836	0.2181	130	0.1618	3251	X-RAY DIFFRACTION	100
2.0836-2.1783	0.1695	146	0.1598	3246	X-RAY DIFFRACTION	99
2.1783-2.293	0.2093	129	0.1575	3290	X-RAY DIFFRACTION	100
2.293-2.4364	0.1929	136	0.1618	3261	X-RAY DIFFRACTION	100
2.4364-2.6241	0.1783	144	0.1693	3286	X-RAY DIFFRACTION	100
2.6241-2.8875	0.2077	136	0.1664	3276	X-RAY DIFFRACTION	100
2.8875-3.3036	0.1735	131	0.1557	3259	X-RAY DIFFRACTION	99
3.3036-4.1559	0.1533	144	0.1475	3303	X-RAY DIFFRACTION	100
4.1559-19.8065	0.1817	146	0.1641	3330	X-RAY DIFFRACTION	99

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	0.2867	-0.0862	-0.2169	0.3481	0.2422	0.3384	0.2706	-0.4722	0.5714	-0.3219	0.048	0.0396	-0.0206	0.1126	0.0192	0.2721	-0.0398	0.0443	0.1932	-0.0173	0.2946	-28.2314	76.5087	90.866
2	0.3367	0.2815	0.1332	0.0061	0.4835	0.1898	-0.1999	0.2859	0.1326	-0.0078	0.021	-0.0794	0.1072	-0.1062	-0.1769	0.1951	-0.0624	0.0464	0.3275	0.0402	0.1839	-20.8728	70.3311	81.3568
3	0.1451	-0.0741	-0.0766	-0.0657	0.0353	0.0578	-0.328	0.4418	0.0265	-0.2419	-0.0098	-0.1036	0.6241	-0.6144	-0.0193	0.3785	-0.1461	0.0719	0.4684	-0.0266	0.3406	-15.4671	63.7158	72.2315
4	0.5483	0.1833	0.1848	0.6571	-0.2697	1.3799	0.014	0.0131	0.0649	-0.0556	0.0387	0.022	-0.0065	0.0897	0.0013	0.173	0.006	-0.0154	0.1914	-0.002	0.1673	-37.8115	59.4974	77.4961
5	0.3892	0.0288	0.2045	0.6892	-0.1728	0.5596	-0.0803	0.0369	0.1736	0.0502	0.0393	0.1997	-0.1732	-0.0292	-0.0001	0.2194	-0.011	-0.0186	0.1991	0.0375	0.2252	-40.7097	70.5529	76.6984
6	0.1182	0.1376	0.064	0.0588	0.1405	0.066	-0.0593	0.252	0.2195	0.0246	-0.0211	0.0209	-0.0456	-0.035	-0.0003	0.2025	0.0174	0.0011	0.2161	0.0012	0.2531	-39.3042	71.9103	87.8484
7	0.1165	0.235	0.2313	0.4007	0.316	0.413	0.1093	-0.0036	-0.1562	0.0911	-0.0487	0.003	-0.0019	0.0225	0.0049	0.1937	0.0019	-0.019	0.191	0.0009	0.1866	-30.784	58.6669	85.2639
8	0.6969	0.0226	0.5635	0.1144	0.2136	0.4877	0.0252	0.0186	0.0295	0.0374	0.0207	-0.0117	-0.048	0.0822	0.0156	0.1884	-0.0103	0.0021	0.1794	0.0226	0.1723	-27.4879	67.4287	87.6826
9	0.3929	0.301	0.0647	0.2768	-0.0643	0.1129	0.0034	-0.0807	-0.1143	0.1625	0.1204	-0.0907	0.1819	-0.0576	0.0001	0.2398	0.0189	-0.0292	0.1814	0.0121	0.2051	-38.2773	52.788	84.8347
10	0.1751	0.0518	0.0824	0.536	0.1023	0.4888	-0.1213	0.0794	0.0095	-0.2938	-0.0051	0.1297	-0.0992	-0.0153	-0.0302	0.2324	0	-0.0134	0.1399	0.0096	0.1953	-4.2822	84.1504	52.2955
11	0.1698	0.3471	0.1144	0.3117	0.3859	-0.0172	-0.029	0.1128	-0.1846	0.0206	-0.028	-0.085	0.0321	-0.185	-0.0002	0.2063	-0.0352	-0.0083	0.3036	0.0074	0.205	-14.8448	72.7481	52.5793
12	0.0922	0.1472	0.0216	0.0041	0.0755	0.1114	0.1174	-0.2387	-0.0363	-0.1002	0.179	0.0977	0.3448	-0.1296	0.0003	0.2338	-0.0193	-0.0172	0.3796	0.0445	0.312	-20.1603	63.2494	53.8372
13	0.6803	-0.0518	-0.3615	0.1686	-0.1324	0.2652	-0.0205	-0.0465	-0.065	0.0832	-0.0572	-0.0531	0.1412	-0.1078	0.0003	0.1803	-0.0039	-0.0047	0.1732	0.0043	0.1811	-6.5193	72.5843	68.6984
14	0.2689	-0.0253	-0.0768	0.4512	-0.2769	0.1389	0.0608	0.0817	-0.0875	0.4459	-0.0606	0.1064	0.8479	0.2149	0.0044	0.3379	-0.0207	0.0509	0.2627	0.0182	0.2544	-4.6018	64.7843	75.7219
15	0.0574	-0.0095	-0.0747	0.113	0.0679	0.1554	-0.0183	-0.5642	-0.0178	0.155	-0.0563	-0.1581	0.1163	-0.0575	0.0001	0.2703	0.0143	-0.0059	0.3061	-0.0218	0.2079	-7.0212	74.692	78.8049
16	0.0463	0.0284	-0.0416	0.1519	-0.1354	0.4735	0.0108	0.0722	-0.0116	0.1596	-0.1068	0.0463	-0.0121	-0.3514	-0.006	0.2082	0.0168	0.0055	0.2073	-0.0195	0.2062	-11.8664	82.826	67.852
17	0.2166	0.007	-0.1061	0.1919	-0.2261	0.2256	-0.0927	-0.1637	0.1658	-0.0377	-0.1876	-0.0542	-0.2566	-0.0989	-0.0465	0.2011	-0.0009	-0.0311	0.1849	-0.0285	0.2008	-2.1399	83.7653	64.5381
18	0.4757	0.1216	-0.0509	0.1826	-0.2163	0.3843	-0.0443	0.1404	-0.0082	-0.0372	-0.0437	-0.1178	0.1694	0.0842	0.0005	0.1877	0.0182	0.0113	0.1797	-0.0073	0.2042	-1.5996	68.2598	61.7693
19	0.1536	0.0171	0.1526	0.212	0.123	0.8507	-0.0494	0.1172	-0.0063	-0.0341	0.0101	-0.0504	0.0503	-0.0586	0	0.1883	-0.0068	0.0038	0.1904	-0.0136	0.1926	-4.6404	74.8351	55.2909
20	0.5016	-0.0091	0.5085	0.3569	0.33	0.7251	-0.0344	-0.0713	-0.167	0.2192	0.0105	-0.2066	0.1195	0.1557	0.0265	0.2315	0.0417	0.0146	0.1932	0.0282	0.2723	3.5649	67.1793	69.0541
21	0.151	0.1223	-0.1254	0.218	0.0586	0.3901	0.0244	0.0412	0.0257	-0.0462	0.0732	-0.1921	0.1002	-0.1076	0.0098	0.1774	0.015	0.0123	0.1714	-0.0058	0.2052	-48.8508	72.0867	52.2341
22	0.0661	0.0139	0.0202	0.2916	0.059	0.2691	0.1155	-0.0754	0.0704	0.0382	-0.1229	-0.0038	0.1395	0.012	-0	0.2042	-0.0197	-0.0112	0.2718	0.0251	0.1714	-41.3048	65.1447	60.5266
23	0.0722	-0.0101	0.0153	0.2073	-0.1394	0.0268	-0.1855	0.5022	-0.275	0.0232	0.3133	-0.2554	0.077	0.2451	-0.0008	0.2865	-0.0201	-0.0229	0.4294	0.0085	0.2512	-32.8125	58.8828	67.3205
24	0.9133	0.0477	0.4477	0.1658	0.0288	0.3326	-0.1108	0.0182	-0.1013	0.0377	-0.0618	-0.164	0.0023	0.1285	-0.0037	0.19	-0.0082	0.0027	0.2294	0.0402	0.1953	-30.7405	66.6033	46.5554
25	1.0608	0.1304	0.3514	0.7611	0.5177	0.4802	-0.0432	0.2909	-0.2484	-0.116	0.029	-0.0846	0.0001	0.3663	-0.0008	0.2244	0.0057	0.0115	0.293	-0.0181	0.2565	-22.5317	64.8915	42.1111
26	0.7767	0.0138	-0.5252	0.2143	0.3602	0.6868	0.137	0.0523	0.2574	-0.0103	-0.0476	0.1001	-0.3205	0.0009	0.0008	0.2413	-0.014	0.0128	0.1906	0.0327	0.2422	-36.5117	75.8141	47.0652
27	2.2253	0.3353	-0.8748	0.6192	-0.4796	1.0839	-0.0798	0.0494	-0.1718	-0.0074	-0.0286	-0.0444	0.1254	-0.1154	-0.0001	0.1877	-0.0282	0.0013	0.1571	0.001	0.1908	-39.965	62.1119	49.262
28	0.39	0.1672	-0.6317	0.1654	-0.093	0.8936	0.2285	0.5803	-0.2887	-0.6431	-0.2124	-0.1549	0.5039	-0.0899	0.0578	0.3423	0.0042	0.0645	0.2653	-0.0896	0.3469	-30.8359	57.6772	38.9022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 38 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 39 through 76 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 77 through 101 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 102 through 112 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 113 through 129 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 130 through 152 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 153 through 168 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 14 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 15 through 28 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 29 through 38 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 39 through 62 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 63 through 76 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 77 through 85 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 86 through 101 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 102 through 112 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 113 through 129 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 130 through 151 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 152 through 168 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 13 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 14 through 28 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 29 through 38 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 39 through 62 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 63 through 85 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 86 through 112 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 113 through 152 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 153 through 168 )

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Yorodumi