PDB-3b49: Crystal structure of an uncharacterized conserved protein from Li...

ID or keywords:

Entry

Database: PDB / ID: 3b49

Title

Crystal structure of an uncharacterized conserved protein from Listeria innocua

Components

Lin2189 protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Big 860.1 / MCSG / SAD / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

GyrI-like cyclopropanoid cyclopropyl hydrolase Lin2189-like / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta / Lin2189 protein

Function and homology information

Biological species

Listeria innocua Clip11262 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.6 Å

Authors

Nocek, B. / Duggan, E. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of an uncharacterized conserved protein from Listeria innocua.
Authors: Nocek, B. / Duggan, E. / Freeman, L. / Joachimiak, A.

History

Deposition	Oct 23, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3b49.cif.gz	62.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3b49.ent.gz	50.6 KB	Display	PDB format
PDBx/mmJSON format	3b49.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/b4/3b49 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b49	HTTPS FTP

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Related structure data

Similar structure data	5vfa-2 4x7q-1 6mlo-d 4fit-1 2yjp-2 5x5r-1 5a76-4 2yjp-3 5x3h-1 1es4-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC87095

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lin2189 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.506, 68.108, 69.853
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lin2189 protein Mass: 25205.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua Clip11262 (bacteria) / Species: Listeria innocua / Strain: Clip11262 / Serovar 6a / Gene: lin2189 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q929T5
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.38 Å³/Da / Density % sol: 48.39 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 1.4M tri-Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007 / Details: Mirrors
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.6→40 Å / Num. all: 31607 / Num. obs: 31607 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / R_merge(I) obs: 0.077 / Net I/σ(I): 26.6
Reflection shell	Resolution: 1.6→1.64 Å / R_merge(I) obs: 0.369 / Mean I/σ(I) obs: 2.1 / % possible all: 82.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL2Map		phasing
SHELXCD		phasing
SHELXE		model building
SHELXD		phasing
ARP/wARP		model building

Refinement

Resolution: 1.6→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.946 / SU B: 2.56 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There is an unmodeled density in the cavity formed by residues: Y46, W85, W99, F154, Y154, E185.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	1009	3.2 %	RANDOM
R_work	0.17	-	-	-
all	0.175	31607	-	-
obs	0.171	31539	97.14 %	-

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: 13.389 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	0 Å²	0 Å²
2-	-	0.55 Å²	0 Å²
3-	-	-	-0.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1685	0	12	295	1992

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1779
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1307
X-RAY DIFFRACTION	r_angle_refined_deg	1.318	1.97	2397
X-RAY DIFFRACTION	r_angle_other_deg	0.802	3	3176
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.837	5	215
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.296	23.605	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.407	15	345
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.912	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	245
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1934
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	367
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	322
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	1327
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	848
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	925
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	172
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.143	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.261	0.2	39
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.166	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	1.13	1.5	1288
X-RAY DIFFRACTION	r_mcbond_other	0.225	1.5	412
X-RAY DIFFRACTION	r_mcangle_it	1.256	2	1693
X-RAY DIFFRACTION	r_scbond_it	2.258	3	854
X-RAY DIFFRACTION	r_scangle_it	3.099	4.5	698

LS refinement shell

Resolution: 1.6→1.642 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.224	55	-
R_work	0.195	1907	-
all	-	1962	-
obs	-	-	83.52 %

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	4.1526	1.2368	-1.0808	10.3358	5.4927	4.4236	0.0075	-0.0376	-0.0536	0.3177	-0.1999	-0.0096	0.0386	-0.3528	0.1924	0.0232	0.0071	0.0205	0.051	-0.0209	0.018	19.9294	9.7906	9.0849
2	0.1675	-0.9715	-0.2687	8.319	-0.6178	2.1953	0.0152	0.1005	0.0015	0.034	-0.0012	0.205	0.1126	-0.4163	-0.014	0.004	-0.0415	0.0106	0.0738	-0.0014	0.0547	21.7998	-3.1029	3.1019
3	0.0945	-0.3604	-0.2808	1.4066	1.045	0.8536	0.0726	0.024	0.074	0.0344	-0.125	0.0955	-0.0005	-0.1203	0.0524	0.0255	-0.0073	-0.0083	0.0691	-0.0003	0.0224	27.5717	7.7441	-2.5036
4	1.9544	-2.2881	0.9294	3.7747	-0.1042	1.4228	-0.0173	-0.0568	0.1388	0.0639	0.1167	-0.0768	0.0343	0.2823	-0.0995	0.0018	0.0183	-0.0051	0.0783	0.0248	0.0543	46.8066	5.5922	4.5451
5	2.8101	-2.1172	-1.0109	2.6832	1.9014	1.5577	0.0026	-0.3148	0.0262	0.1514	0.0552	-0.0852	0.007	0.1079	-0.0578	0.0302	0.0071	-0.0048	0.0737	0.023	0.0242	44.4051	9.5097	11.739
6	5.8695	-3.4816	-1.7631	2.0655	1.0633	1.2718	-0.0303	-0.2452	0.3586	-0.0343	0.1626	-0.3652	0.0555	0.0268	-0.1323	0.0069	-0.0007	0.0354	0.0834	-0.0646	0.0306	30.2643	23.6278	15.433
7	1.7617	-1.7986	-0.8919	2.9066	1.2575	0.564	0.1548	-0.015	-0.0089	-0.1615	-0.1692	-0.0178	-0.1073	-0.0055	0.0144	0.0834	0.0229	0.0159	0.0464	-0.0162	0.0051	27.8591	15.584	9.5279
8	1.9695	-0.4801	0.9448	1.8911	0.4031	4.6443	-0.0136	0.2786	-0.0221	0.0411	-0.0433	-0.0264	0.057	0.1726	0.0569	0.0039	0.0159	0.0235	0.0619	0.0025	0.0578	44.8247	1.1224	-2.8104
9	8.3683	-0.2698	4.3341	6.7692	-1.6605	2.5868	0.3302	0.41	-1.1347	-0.0693	-0.0252	-0.4263	0.8989	0.4416	-0.3049	0.1072	0.1254	0.0356	-0.0208	-0.024	0.1802	47.7829	-7.1201	0.456
10	1.8204	-1.1334	-0.3754	0.8666	0.1781	0.8876	-0.06	0.0361	0.0247	0.0712	0.0201	-0.033	0.0441	0.0902	0.0398	0.0254	0.0022	0.0062	0.0461	0.0105	0.0523	41.4005	5.1117	3.3531
11	10.1041	1.8795	-0.6556	4.7438	0.3068	0.0844	0.1884	0.2465	0.1194	0.2326	-0.1088	0.0393	-0.1947	-0.1543	-0.0796	0.0524	0.0213	0.0098	0.0283	-0.0069	0.0235	28.8412	21.1835	3.7721
12	6.9937	0.1272	3.3878	1.2284	0.9469	9.1257	-0.0376	-0.1847	0.522	-0.0604	-0.0134	0.0061	-0.3316	-0.074	0.051	0.023	-0.0188	0.0408	0.014	-0.0486	0.0968	36.7821	26.8871	7.663
13	1.2448	0.4033	-0.7583	4.151	0.72	0.6939	0.08	-0.2154	-0.0623	0.2269	-0.1192	0.0777	-0.0162	0.201	0.0392	0.0181	-0.0176	0.005	0.1	-0.0336	0.0253	44.301	22.183	13.1633
14	1.5648	2.3099	1.9798	4.0264	2.9838	3.7225	-0.081	0.2717	0.0351	-0.2162	0.0696	-0.0765	-0.1768	0.1347	0.0114	0.0229	0.0022	0.0089	0.056	0.0131	0.0246	32.2636	12.9217	-3.59
15	1.1588	-0.5201	0.4616	0.4675	-0.9788	4.876	-0.0458	0.0719	-0.1424	0.0279	-0.0076	0.0615	0.2225	0.1128	0.0534	0.0654	-0.0223	0.0101	0.0092	-0.0109	0.0295	30.5401	-6.8924	4.2252
16	1.5462	-0.443	1.809	0.1896	-1.0277	6.2536	-0.0947	0.1382	-0.2236	0.0231	0.0185	0.0292	0.4365	0.1384	0.0762	0.1077	-0.0121	0.0372	0.0001	-0.0649	0.0661	31.441	-12.3736	-1.3315
17	4.2494	1.0793	-5.5291	5.2126	-4.1015	8.6673	-0.1249	0.3633	-0.1385	-0.2998	0.0606	-0.1318	0.132	-0.3793	0.0642	0.0526	-0.039	0.0042	0.0761	-0.1155	0.0127	28.237	-9.3425	-12.8119
18	0.5011	0.1966	-0.3609	0.4196	0.545	1.6367	-0.0538	0.0537	-0.1303	0.0237	0.0268	-0.0448	0.0461	0.0369	0.027	0.0428	-0.0069	0.0145	0.0499	-0.013	0.0306	35.1358	0.3389	-2.2988
19	2.0179	2.5929	2.0411	9.5157	-2.5814	6.4442	-0.0654	0.1013	-0.0556	0.1235	-0.2288	-0.1843	-0.1549	0.3955	0.2942	0.0367	-0.0221	-0.0085	0.0424	0.0488	0.0225	32.697	-4.1091	18.2258
20	0.4935	-0.0914	-0.6273	0.6014	-1.568	5.6512	-0.0024	0.0845	-0.2085	0.0137	-0.069	0.0559	0.1248	0.0346	0.0714	0.0461	-0.0218	0.0058	0.0401	-0.0102	0.0314	30.0046	-2.6097	-0.6664

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	5 - 13	8 - 16
2	X-RAY DIFFRACTION	2	A	A	14 - 22	17 - 25
3	X-RAY DIFFRACTION	3	A	A	23 - 34	26 - 37
4	X-RAY DIFFRACTION	4	A	A	35 - 41	38 - 44
5	X-RAY DIFFRACTION	5	A	A	42 - 55	45 - 58
6	X-RAY DIFFRACTION	6	A	A	56 - 69	59 - 72
7	X-RAY DIFFRACTION	7	A	A	70 - 84	73 - 87
8	X-RAY DIFFRACTION	8	A	A	85 - 88	88 - 91
9	X-RAY DIFFRACTION	9	A	A	89 - 96	92 - 99
10	X-RAY DIFFRACTION	10	A	A	97 - 106	100 - 109
11	X-RAY DIFFRACTION	11	A	A	107 - 113	110 - 116
12	X-RAY DIFFRACTION	12	A	A	114 - 121	117 - 124
13	X-RAY DIFFRACTION	13	A	A	122 - 135	125 - 138
14	X-RAY DIFFRACTION	14	A	A	136 - 143	139 - 146
15	X-RAY DIFFRACTION	15	A	A	144 - 156	147 - 159
16	X-RAY DIFFRACTION	16	A	A	157 - 167	160 - 170
17	X-RAY DIFFRACTION	17	A	A	168 - 174	171 - 177
18	X-RAY DIFFRACTION	18	A	A	175 - 188	178 - 191
19	X-RAY DIFFRACTION	19	A	A	189 - 199	192 - 202
20	X-RAY DIFFRACTION	20	A	A	200 - 208	203 - 211

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