PDB-6ntr: Crystal Structure of Beta-barrel-like Protein of Domain of Unknow...

ID or keywords:

Entry

Database: PDB / ID: 6ntr

Title

Crystal Structure of Beta-barrel-like Protein of Domain of Unknown Function DUF1849 from Brucella abortus

Components

ATP/GTP-binding site-containing protein A

Keywords

UNKNOWN FUNCTION / beta barrel-like fold / beta-structure / cell envelope integrity / Chicago Center for Functional Annotation / Midwest Center for Structural Genomics / MCSG / PSI-Biology

Function / homology

EipB-like / EipB-like / ATP/GTP-binding site-containing protein A

Function and homology information

Biological species

Brucella abortus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.101 Å

Authors

Kim, Y. / Bigelow, L. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: J.Bacteriol. / Year: 2019
Title: BrucellaPeriplasmic Protein EipB Is a Molecular Determinant of Cell Envelope Integrity and Virulence.
Authors: Herrou, J. / Willett, J.W. / Fiebig, A. / Czyz, D.M. / Cheng, J.X. / Ultee, E. / Briegel, A. / Bigelow, L. / Babnigg, G. / Kim, Y. / Crosson, S.

History

Deposition	Jan 30, 2019	Deposition site: RCSB / Processing site: RCSB
Supersession	Feb 13, 2019	ID: 5UC2
Revision 1.0	Feb 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2019	Group: Data collection / 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
Revision 1.2	Jun 5, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ntr.cif.gz	402.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ntr.ent.gz	348.4 KB	Display	PDB format
PDBx/mmJSON format	6ntr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ntr_validation.pdf.gz	485.8 KB	Display	wwPDB validaton report
Full document	6ntr_full_validation.pdf.gz	515.6 KB	Display
Data in XML	6ntr_validation.xml.gz	39.5 KB	Display
Data in CIF	6ntr_validation.cif.gz	53.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/6ntr ftp://data.pdbj.org/pub/pdb/validation_reports/nt/6ntr	HTTPS FTP

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Related structure data

Similar structure data	2cis-d 3qjj-1 4mc3-d 7aru-d 6apj-1 2htb-2 2htb-4 4p94-d 1vqr-1 2htb-1 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 - HomologyF&H Search
Other databases	TargetTrack: APC114214

Similar structure data

Other databases

TargetTrack: APC114214

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ATP/GTP-binding site-containing protein A

B: ATP/GTP-binding site-containing protein A

C: ATP/GTP-binding site-containing protein A

D: ATP/GTP-binding site-containing protein A

hetero molecules

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

1

A: ATP/GTP-binding site-containing protein A

hetero molecules

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

2

B: ATP/GTP-binding site-containing protein A

hetero molecules

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

3

C: ATP/GTP-binding site-containing protein A

hetero molecules

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

4

D: ATP/GTP-binding site-containing protein A

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.360, 69.240, 83.239
Angle α, β, γ (deg.)	90.09, 90.02, 78.66
Int Tables number	1
Space group name H-M	P1

#1: Protein	ATP/GTP-binding site-containing protein A / DUF1849 Mass: 29047.471 Da / Num. of mol.: 4 / Fragment: UNP residues 29-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus (bacteria) / Gene: BAUG_2423 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Gold / References: UniProt: A0A0M1WBA0
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.33 Å³/Da / Density % sol: 47.29 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MCSG2 F10: 24% w/v PEG1500, 20% w/v glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 57342 / % possible obs: 94.9 % / Redundancy: 2.8 % / R_merge(I) obs: 0.068 / Net I/σ(I): 19.96
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 1.47 / % possible all: 68.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.101→35.234 Å / Cross valid method: FREE R-VALUE / σ(F): 2.66 / Phase error: 32.16

	R_factor	Num. reflection	% reflection
R_free	0.2447	2916	5.09 %
R_work	0.1945	-	-
obs	0.2018	57339	94.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.101→35.234 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7678	0	48	129	7855

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	7893
X-RAY DIFFRACTION	f_angle_d	1.474	10609
X-RAY DIFFRACTION	f_dihedral_angle_d	23.464	3002
X-RAY DIFFRACTION	f_chiral_restr	0.089	1159
X-RAY DIFFRACTION	f_plane_restr	0.008	1388

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 (%)
2.1018-2.138	0.3367	123	0.3271	1935	X-RAY DIFFRACTION	64
2.138-2.1769	0.3035	126	0.3117	2317	X-RAY DIFFRACTION	76
2.1769-2.2187	0.3509	123	0.2985	2511	X-RAY DIFFRACTION	85
2.2187-2.264	0.3345	142	0.3183	2711	X-RAY DIFFRACTION	90
2.264-2.3132	0.4033	138	0.3141	2820	X-RAY DIFFRACTION	93
2.3132-2.367	0.3608	143	0.3239	2829	X-RAY DIFFRACTION	93
2.367-2.4261	0.3229	132	0.3143	2759	X-RAY DIFFRACTION	93
2.4261-2.4917	0.3597	156	0.3172	2826	X-RAY DIFFRACTION	93
2.4917-2.565	0.3311	161	0.3126	2773	X-RAY DIFFRACTION	93
2.565-2.6477	0.3326	146	0.3214	2850	X-RAY DIFFRACTION	93
2.6477-2.7422	0.3153	144	0.3112	2840	X-RAY DIFFRACTION	94
2.7422-2.8519	0.3434	153	0.2953	2768	X-RAY DIFFRACTION	93
2.8519-2.9816	0.2865	150	0.2732	2864	X-RAY DIFFRACTION	94
2.9816-3.1386	0.2691	162	0.2503	2798	X-RAY DIFFRACTION	93
3.1386-3.3349	0.27	149	0.2257	2822	X-RAY DIFFRACTION	94
3.3349-3.5919	0.2227	114	0.1932	2864	X-RAY DIFFRACTION	95
3.5919-3.9525	0.2245	156	0.1722	2841	X-RAY DIFFRACTION	94
3.9525-4.5223	0.1867	127	0.1378	2836	X-RAY DIFFRACTION	95
4.5223-5.6895	0.1808	142	0.1211	2868	X-RAY DIFFRACTION	95
5.6895-27.7487	0.2371	134	0.1579	2664	X-RAY DIFFRACTION	88

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	1.5344	0.0055	-1.058	3.9382	-2.335	2.4824	-0.2902	0.0314	-0.0793	0.1905	-0.1716	-0.1622	-0.1285	-0.0735	0.5087	0.6106	-0.0577	-0.1066	0.2513	-0.0042	0.5167	91.4108	-18.7964	39.3559
2	2.649	-1.8282	2.6875	5.0897	-3.1105	3.1738	0.3181	-0.0338	-0.4043	0.1168	0.023	0.3238	0.3271	0.0666	-0.0784	0.6019	-0.0973	-0.0764	0.3025	0.0679	0.5661	94.1156	-25.3806	40.5988
3	1.9698	0.4561	0.8186	3.7249	0.6509	2.0596	0.1047	-0.0608	-0.3419	-0.0281	0.0268	-0.7648	0.2952	0.437	-0.1448	0.7666	-0.0091	-0.0762	0.2476	-0.0096	0.6888	105.6159	-29.0508	42.6882
4	5.4886	-6.5153	-4.2307	8.8865	3.4085	5.542	0.0987	-0.1861	-0.6679	-0.5562	-0.0752	0.5605	0.3643	-0.1255	0.0041	0.6968	-0.1156	0.0095	0.3378	-0.0449	0.4081	99.1601	-13.9271	55.6907
5	4.7408	1.7169	0.742	3.9081	0.4405	2.2525	-0.023	0.2094	-0.182	0.0033	0.1433	0.0597	-0.1219	0.0605	-0.1502	0.5753	-0.0619	-0.0658	0.2163	-0.0395	0.4444	95.7185	-12.1505	44.6413
6	5.9057	1.749	-4.0087	5.3568	-2.9245	3.3363	0.0606	0.5571	-0.0091	0.2175	0.4884	1.0008	-0.3574	-0.9203	-0.1327	0.5844	0.0903	0.0341	0.2774	0.2595	0.7042	58.2688	21.7931	42.9233
7	3.1032	1.2971	-2.0747	1.6377	-0.2261	2.1996	0.3764	0.2464	0.409	0.6915	-0.1677	0.2638	-0.9865	-0.2332	-0.2911	0.7531	-0.0873	-0.0394	0.3113	0.1184	0.6445	58.7909	17.6795	55.0846
8	4.5973	1.7484	-3.283	3.5886	-2.6846	6.6601	0.0692	0.1841	0.5797	0.6942	0.2436	-0.0455	-0.3994	-0.2879	-0.1894	0.8916	-0.0072	0.0518	0.3763	0.0806	0.4695	66.0656	22.33	47.6513
9	4.3427	0.4007	-2.7908	3.7828	-0.1538	2.7632	0.0854	-0.7099	-0.151	0.8993	-0.3073	-0.614	-0.2544	0.8887	0.0336	0.7804	-0.1263	-0.1094	0.3603	-0.0263	0.6879	68.2243	19.5372	54.8005
10	5.5306	0.9183	1.6052	4.0734	-0.8946	4.1955	-0.3976	-0.0929	0.164	0.3692	0.0963	-0.3844	-0.009	0.5875	0.1848	0.4874	-0.0722	-0.0755	0.3245	-0.0375	0.5287	79.2342	14.2133	49.0961
11	4.6061	5.0956	4.113	7.6022	2.3184	6.1983	-0.5892	0.7807	0.1641	-0.5727	0.4832	0.1246	0.1854	-0.7571	0.1051	0.6003	-0.2097	0.0016	0.5702	0.0689	0.4497	63.3847	8.9946	34.8231
12	6.2176	1.3919	1.2534	3.1602	-0.9391	3.9728	0.3807	-0.1646	-0.2473	0.2499	-0.1863	-0.4183	0.807	-0.3875	-0.1342	0.5359	-0.0657	-0.0552	0.2716	-0.0667	0.5211	67.2014	4.8029	44.5142
13	0.0408	-0.1	-0.266	3.5467	0.032	1.4618	-0.2437	-0.1909	0.2179	-0.2651	0.2818	0.583	0.288	-0.7984	0.0308	0.6691	-0.1512	-0.0623	0.5526	0.0251	0.6268	50.4542	15.087	39.9397
14	3.0722	-0.3999	-0.1909	7.135	-2.7798	4.6164	0.4877	0.286	0.3097	0.1519	0.1255	0.7341	0.487	-0.2682	-0.5918	0.6788	-0.1559	-0.1002	0.2857	-0.048	0.4535	56.9607	9.1196	44.6176
15	4.7698	4.1234	-5.3111	5.0471	-6.456	8.4243	0.3536	0.9666	1.2625	0.6389	0.7318	0.7014	-0.4994	-0.6621	-0.814	0.8554	-0.0143	0.0748	0.6372	0.1801	0.8147	56.405	18.8136	48.5604
16	0.4797	0.5157	0.184	0.624	-0.0051	0.9749	0.1793	0.183	-0.6875	0.0394	-0.3057	-0.2616	0.1364	-0.0271	-0.174	1.0295	0.0338	-0.4178	0.1977	-0.2283	1.0044	80.4318	-34.123	90.7692
17	3.3385	0.4986	3.8853	0.7551	-0.0434	6.04	0.2774	-0.2379	-0.2932	0.4223	-0.0003	0.1327	0.473	-0.1498	-0.3001	0.9787	-0.1327	-0.1646	0.3049	-0.018	0.7829	70.1004	-35.8279	92.9897
18	6.4029	1.5387	-1.0897	3.1256	0.7704	5.1615	-0.0154	0.0926	0.0787	0.1305	-0.0608	0.5867	-0.2145	-0.1613	0.1216	0.5838	-0.0387	-0.0555	0.3087	-0.053	0.4987	65.278	-23.9275	85.1694
19	3.4701	-0.117	0.6542	4.6231	1.1621	3.5269	-0.122	0.9257	-0.5157	0.1645	0.3314	-0.2986	0.0504	0.5293	-0.0776	0.5374	-0.1163	-0.1273	0.5053	-0.211	0.6515	82.2389	-26.8646	83.4864
20	3.8171	-0.1174	-0.4414	7.8747	1.6349	4.0777	0.3932	0.3023	-0.4322	0.7214	0.2278	-1.1411	-0.2668	0.4369	-0.5168	0.6418	-0.0498	-0.1637	0.3074	-0.0755	0.6309	80.8745	-27.1339	89.545
21	1.9265	0.3658	-0.0922	2.0004	-0.4893	5.2335	-0.283	0.0596	0.069	0.0138	-0.2203	-0.3487	0.0727	-0.1239	0.4924	0.5592	-0.0491	-0.0187	0.2565	-0.0493	0.5377	94.8754	3.7587	80.6879
22	2.4259	-0.5094	-0.9947	4.1649	-1.0448	3.9758	0.0632	0.1635	-0.0176	0.0104	-0.1474	0.2033	-0.1773	-0.0319	0.1144	0.6607	0.0072	-0.0682	0.1776	-0.0655	0.6268	86.8865	13.1724	80.9933
23	2.4356	-2.9885	1.4494	8.4586	-1.4912	3.805	-0.2672	-0.431	-0.024	0.8651	0.2423	0.9924	-0.4854	-0.4958	0.0734	0.5927	-0.0218	0.1313	0.2837	-0.0233	0.5841	78.2242	4.8931	91.9332
24	5.8646	2.5025	-0.3491	3.2507	0.0751	3.7828	-0.0829	0.0802	-0.0902	-0.0135	0.1536	-0.2794	0.4942	0.1768	-0.0942	0.6055	-0.0542	-0.0364	0.2113	0.0415	0.4487	94.4348	-3.4228	85.9944

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 84 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 153 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 166 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 167 through 270 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 31 through 44 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 45 through 67 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 68 through 83 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 84 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 153 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 154 through 166 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 167 through 186 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 187 through 210 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 211 through 249 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 250 through 271 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 30 through 67 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 68 through 117 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 118 through 176 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 177 through 223 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 224 through 271 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 30 through 67 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 68 through 128 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 129 through 186 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 187 through 270 )

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