PDB-5do8: 1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 ...

ID or keywords:

Entry

Database: PDB / ID: 5do8

Title

1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 alpha-1,6-glucosidase

Components

Lmo0184 protein

Keywords

HYDROLASE / Glycoside Hydrolase Family 13 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

oligosaccharide catabolic process / alpha-amylase activity
Similarity search - Function

Biological species

Listeria monocytogenes serovar 1/2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Light, S.H. / Halavaty, A.S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.

History

Deposition	Sep 10, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5do8.cif.gz	711.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5do8_validation.pdf.gz	469.1 KB	Display	wwPDB validaton report
Full document	5do8_full_validation.pdf.gz	474.8 KB	Display
Data in XML	5do8_validation.xml.gz	74 KB	Display
Data in CIF	5do8_validation.cif.gz	113.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/do/5do8 ftp://data.pdbj.org/pub/pdb/validation_reports/do/5do8	HTTPS FTP

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Related structure data

Related structure data	4kmqC 5f7pC 5f7qC 5f7rC 5f7sC 5f7uC 5f7vC 1uokS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	20282 4e45-d 5wa0-d 1g5c-d 3jry-d 5cxk-d 3ntj-d 4qs5-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP95188

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3) #138 - Jun 2011 Glucansucrase similarity (3) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

B: Lmo0184 protein

A: Lmo0184 protein

C: Lmo0184 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	88.123, 103.937, 193.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Lmo0184 protein

Mass: 65337.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0184 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q8YAE6

#2: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#3: Chemical

ChemComp-CL / CHLORIDE ION

Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

#4: Chemical

ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER

Mass: 209.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1761 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.67 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Crystallization condition: JCSG+ H8 (Qiagen) 0.1 M Am Acetate, 0.1 M Bis-tris (pH 5.5), 17% Peg 10000 Protein condition: 9 mg/ml + 10 mM Tris (pH 8.3), 500 mM NaCl, 50 mM glucose

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 162894 / % possible obs: 99.6 % / Redundancy: 6.7 % / R_merge(I) obs: 0.109 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.741 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UOK

1uok

Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.952 / SU B: 4.673 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18837	7982	4.9 %	RANDOM
R_work	0.15355	-	-	-
obs	0.15525	154761	99.14 %	-

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: 22.386 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.23 Å²	0 Å²	-0 Å²
2-	-	-0.58 Å²	-0 Å²
3-	-	-	0.81 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13737	0	82	1761	15580

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	14353
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	12940
X-RAY DIFFRACTION	r_angle_refined_deg	1.38	1.943	19500
X-RAY DIFFRACTION	r_angle_other_deg	0.959	3	29901
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.192	5	1698
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.083	25.352	809
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.875	15	2466
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.897	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	2000
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	16553
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3425
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.54	1.403	6708
X-RAY DIFFRACTION	r_mcbond_other	0.54	1.403	6707
X-RAY DIFFRACTION	r_mcangle_it	0.928	2.1	8407
X-RAY DIFFRACTION	r_mcangle_other	0.928	2.1	8408
X-RAY DIFFRACTION	r_scbond_it	0.714	1.488	7645
X-RAY DIFFRACTION	r_scbond_other	0.714	1.488	7645
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.18	2.2	11085
X-RAY DIFFRACTION	r_long_range_B_refined	5.402	12.901	18824
X-RAY DIFFRACTION	r_long_range_B_other	5.402	12.903	18825
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.803→1.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	554	-
R_work	0.223	10793	-
obs	-	-	94.38 %

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	7.3518	-2.1016	-1.3925	3.2483	-0.0931	3.3971	0.3085	-0.033	0.7001	-0.0918	-0.1681	-0.0791	-0.475	0.0741	-0.1404	0.0815	-0.0025	0.0157	0.0453	-0.0195	0.0847	-30.9988	-11.9466	-36.4227
2	0.6798	-0.0646	-0.2832	0.3914	-0.0882	0.8634	-0.0019	-0.1218	0.0129	0.0849	0.0323	-0.0396	0.0073	0.1144	-0.0305	0.0386	0.0083	-0.0087	0.0811	-0.0173	0.0077	-23.9684	-29.0747	-25.3228
3	1.6465	0.6698	0.6861	2.643	1.4572	3.4135	0.0116	-0.3574	-0.1506	0.3514	0.0022	0.1487	0.1954	-0.073	-0.0138	0.0941	0.0268	0.0623	0.0985	0.0579	0.0626	-47.8975	-38.4993	-11.059
4	1.1369	0.0078	0.0349	1.1468	-0.0348	0.3307	-0.0657	-0.1308	-0.0251	0.0797	0.0581	0.1198	0.0334	-0.0062	0.0075	0.056	0.0106	0.0256	0.0756	-0.0073	0.0229	-44.9035	-26.9734	-20.2073
5	0.7855	-0.263	-0.0307	1.2379	0.6065	0.9498	-0.0098	-0.0037	0.0075	0.0648	-0.0071	0.0688	0.0376	-0.05	0.0169	0.0211	-0.0071	0.0004	0.0486	-0.0019	0.0142	-45.2091	-22.9413	-35.1762
6	0.5828	-0.1298	-0.0489	0.6149	-0.1621	0.4892	0.0013	0.014	-0.045	0.0031	-0.0035	0.0385	0.0411	-0.0097	0.0023	0.0158	-0.0007	-0.0002	0.0313	-0.0083	0.0066	-35.7643	-31.8544	-45.4452
7	3.599	1.598	0.288	1.7741	1.0998	2.695	0.053	-0.1601	-0.1809	0.1834	-0.0504	0.0295	0.1834	-0.0758	-0.0025	0.086	0.0095	0.02	0.0316	0.0245	0.0649	-39.9509	-51.6151	-31.8125
8	0.713	0.1391	-0.1593	0.5653	-0.0856	0.4829	-0.0352	-0.0104	-0.0645	-0.0091	0.0135	-0.0542	0.0706	0.058	0.0217	0.0208	0.0171	-0.0029	0.0399	-0.014	0.0164	-23.0125	-36.5758	-42.1999
9	0.8013	-0.2705	0.0803	1.2856	0.3883	1.5022	0.0396	0.0851	0.0666	-0.0964	-0.0262	0.0901	0.0019	-0.124	-0.0134	0.0211	0.0045	-0.0019	0.0579	0.0165	0.0201	-40.118	-20.5852	-58.3694
10	1.5856	-0.3466	-0.086	3.7155	-0.8488	2.609	0.0896	0.1421	0.1479	-0.1752	-0.0251	-0.0663	-0.1008	0.1096	-0.0645	0.0233	0.006	0.013	0.0545	0.0147	0.0167	-30.9946	-21.059	-63.3006
11	1.5297	1.1664	-0.1173	2.8411	0.0364	1.1285	-0.0148	0.0815	-0.1371	-0.0935	-0.0332	-0.1541	0.055	0.011	0.048	0.0277	0.0096	0.0167	0.0647	-0.0177	0.0281	18.4457	-20.0242	-43.6276
12	0.9751	-0.147	0.4878	0.5188	-0.2105	0.7375	-0.0251	0.1235	-0.0012	-0.0419	0.0365	-0.036	-0.0228	0.0455	-0.0115	0.028	-0.0085	0.0186	0.0646	-0.0068	0.0129	18.6052	-16.933	-51.2456
13	1.5503	-0.3626	-0.6744	2.2433	1.08	3.304	0.0223	0.2617	0.1099	-0.2529	0.013	0.1766	-0.1894	-0.1645	-0.0353	0.0511	0.0022	-0.0317	0.0964	0.0571	0.0586	-5.7298	-6.2598	-62.9118
14	0.8471	-0.1389	0.0439	0.7128	-0.0738	0.3799	-0.0231	0.114	0.0386	-0.0718	0.0368	0.0551	-0.0296	-0.0486	-0.0137	0.0268	-0.0054	-0.0048	0.0795	0.0106	0.0112	-0.4295	-16.3932	-57.0479
15	1.3267	-0.1556	-0.2289	0.6646	-0.0918	0.601	-0.0285	0.0319	-0.0111	0.0539	0.0067	0.0406	0.0057	-0.0674	0.0217	0.0323	-0.0147	0.0154	0.0697	-0.0125	0.0381	-3.0521	-24.4794	-48.3762
16	0.2606	0.7169	-0.2706	2.3056	-0.2896	0.9212	0.015	0.047	0.0663	0.0007	0.0446	0.2022	-0.0509	-0.1806	-0.0596	0.0462	0.0093	0.0161	0.1084	-0.0072	0.0768	-1.6143	-16.1468	-30.4117
17	0.6445	0.0912	-0.0261	0.8021	-0.093	0.8647	0.0106	-0.0128	0.0242	0.0309	-0.024	-0.002	-0.0149	-0.0153	0.0134	0.0226	-0.0032	0.0147	0.0169	-0.0046	0.0117	12.1041	-16.3903	-29.7879
18	4.2747	-0.917	-0.7323	2.7345	1.4129	3.0086	0.0496	0.2003	0.2528	-0.1271	-0.0364	0.1087	-0.3666	-0.1389	-0.0132	0.1085	0.0374	0.0212	0.0275	0.0366	0.0735	3.1985	5.4424	-40.3668
19	0.9975	-0.5006	0.2729	1.0005	-0.3342	0.6927	-0.0108	0.0066	0.1014	0.0678	-0.0009	-0.0379	-0.1283	0.0909	0.0117	0.0521	-0.0165	0.0144	0.0216	-0.0081	0.0231	20.5094	-6.8771	-33.2727
20	1.1521	-0.0168	-0.0419	1.58	0.4994	1.488	0.0217	-0.125	-0.132	0.1826	-0.0312	0.0135	0.2088	-0.0858	0.0096	0.0787	-0.0182	0.0171	0.0362	0.013	0.029	9.6697	-28.9733	-17.0564
21	1.2604	-0.001	0.2337	1.2105	0.1457	1.0876	0.0112	-0.1551	-0.125	0.052	-0.0076	0.0668	0.0372	-0.0358	-0.0037	0.0222	-0.0031	0.0054	0.1185	-0.0555	0.0664	-44.5621	-72.534	0.8736
22	1.4542	0.923	-0.0793	1.3417	0.1174	0.5172	-0.0046	0.0315	-0.0327	0.0248	-0.0433	0.078	-0.0482	-0.0963	0.0479	0.0303	0.0083	0.0029	0.1007	-0.0625	0.0454	-39.0935	-60.0194	4.3728
23	0.8236	-0.6151	-0.7355	2.1339	1.3898	3.2957	0.0281	0.0865	0.1003	-0.1237	0.0324	-0.2327	-0.1933	0.0617	-0.0605	0.0348	-0.0241	0.0116	0.0626	-0.0236	0.0548	-18.2085	-47.4636	-0.5599
24	1.1114	-0.0234	0.0399	0.9682	-0.0843	0.432	-0.0687	0.0229	-0.1452	-0.0282	0.0524	-0.1072	0.0167	0.0259	0.0163	0.0579	0.0027	0.0138	0.1142	-0.0638	0.0771	-22.0312	-64.9995	6.9807
25	0.6749	-1.0534	0.5722	3.0547	-2.3658	2.4613	0.0007	0.1224	-0.0219	0.0109	-0.0979	-0.3112	-0.0413	0.2296	0.0972	0.0561	0.0237	0.0119	0.2015	-0.1438	0.2208	-21.0456	-79.5039	-11.1807
26	0.8914	-0.3677	0.0574	1.1956	-0.0873	0.937	0.0186	0.0694	-0.2128	-0.0029	0.006	-0.0016	0.0558	0.067	-0.0246	0.0214	0.0144	-0.0115	0.0957	-0.0842	0.1065	-34.8148	-81.3375	-9.5256
27	4.5822	-0.0411	-0.3747	1.6774	-0.5217	3.3242	0.0497	0.3357	0.0894	-0.2366	-0.064	0.0176	-0.1032	0.2111	0.0143	0.0891	-0.0066	0.0065	0.1546	-0.0356	0.02	-28.5597	-60.5001	-22.7316
28	1.2329	0.4435	0.0295	0.8804	-0.1198	0.7043	-0.0345	0.0911	-0.0334	-0.08	0.0421	0.1027	0.0094	-0.0294	-0.0076	0.0377	0.0096	-0.0124	0.1083	-0.0722	0.0706	-45.5269	-73.5657	-14.3366
29	2.2448	-0.1504	-0.3074	1.4498	0.3155	3.2654	0.0472	-0.049	-0.4685	0.0779	0.0486	-0.0864	0.2626	0.173	-0.0958	0.0772	0.0388	-0.0361	0.0506	-0.0681	0.2572	-28.7489	-96.5539	-6.3631
30	2.8218	0.4163	-0.4606	2.3444	-1.0642	3.4949	-0.0161	-0.0337	-0.558	-0.0336	0.0051	-0.1002	0.4204	0.0351	0.011	0.0822	0.0197	-0.0314	0.0556	-0.0948	0.2981	-35.9568	-101.1232	-10.5709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 12
2	X-RAY DIFFRACTION	2	A	13 - 109
3	X-RAY DIFFRACTION	3	A	110 - 152
4	X-RAY DIFFRACTION	4	A	153 - 250
5	X-RAY DIFFRACTION	5	A	251 - 290
6	X-RAY DIFFRACTION	6	A	291 - 379
7	X-RAY DIFFRACTION	7	A	380 - 401
8	X-RAY DIFFRACTION	8	A	402 - 473
9	X-RAY DIFFRACTION	9	A	474 - 522
10	X-RAY DIFFRACTION	10	A	523 - 554
11	X-RAY DIFFRACTION	11	B	3 - 30
12	X-RAY DIFFRACTION	12	B	31 - 109
13	X-RAY DIFFRACTION	13	B	110 - 152
14	X-RAY DIFFRACTION	14	B	153 - 213
15	X-RAY DIFFRACTION	15	B	214 - 276
16	X-RAY DIFFRACTION	16	B	277 - 314
17	X-RAY DIFFRACTION	17	B	315 - 376
18	X-RAY DIFFRACTION	18	B	377 - 401
19	X-RAY DIFFRACTION	19	B	402 - 466
20	X-RAY DIFFRACTION	20	B	467 - 555
21	X-RAY DIFFRACTION	21	C	4 - 50
22	X-RAY DIFFRACTION	22	C	51 - 112
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