PDB-5euv: Crystal structure of a cold-adapted dimeric beta-D-galactosidase ...

ID or keywords:

Entry

Database: PDB / ID: 5euv

Title

Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain

Components

Beta-D-galactosidase

Keywords

HYDROLASE / beta-D-galactosidase / dimeric / cold-adapted /

enzyme /

glycosyl hydrolase / native

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Paracoccus sp. 32d (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Rutkiewicz-Krotewicz, M. / Bujacz, A. / Pietrzyk, A.J. / Sekula, B. / Bujacz, G.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d.
Authors: Rutkiewicz-Krotewicz, M. / Pietrzyk-Brzezinska, A.J. / Sekula, B. / Cieslinski, H. / Wierzbicka-Wos, A. / Kur, J. / Bujacz, A.

History

Deposition	Nov 19, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Data collection / Database references / Category: citation / diffrn_source Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jan 10, 2018	Group: Database references / Category: citation / citation_author
Revision 1.3	Jan 10, 2024	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	5euv.cif.gz	577.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5euv.ent.gz	478.7 KB	Display	PDB format
PDBx/mmJSON format	5euv.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/eu/5euv ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5euv	HTTPS FTP

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Related structure data

Related structure data	5ldrC 3gm8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ldr-d 5w81-d 5ae6-d 20945 0606 5a7m-d 5ofp-1 1dxr-d 2prc-d 3qgd-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (12) #39 - Mar 2003 lac Repressor similarity (12)

Deposited unit

A: Beta-D-galactosidase

B: Beta-D-galactosidase

hetero molecules

165 kDa, 2 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)	78.490, 106.240, 199.390
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-D-galactosidase Mass: 81844.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus sp. 32d (bacteria) / Plasmid: pBAD-Myc-His A / Production host: Escherichia coli (E. coli) / Strain (production host): LMD194 / References: UniProt: D1LZK0
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 870 / 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: 2.54 Å³/Da / Density % sol: 51.65 % / Description: rectangular prism
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 24% PEG MME 2000, 0.1M ammonium acetate, Bis-Tris pH 6.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2013
Radiation	Monochromator: SI (111), mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.967 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. all: 65993 / Num. obs: 65576 / % possible obs: 99.4 % / Redundancy: 4.39 % / R_merge(I) obs: 0.12 / Net I/σ(I): 11.67
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 3.94 % / R_merge(I) obs: 0.71 / Mean I/σ(I) obs: 2.07 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
XDS		data reduction
XDS		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GM8

3gm8

Resolution: 2.4→45.77 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.922 / SU B: 18.533 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23088	3280	5 %	RANDOM
R_work	0.16525	-	-	-
obs	0.16856	62295	99.36 %	-

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: 36.872 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.93 Å²	-0 Å²	-0 Å²
2-	-	4.15 Å²	-0 Å²
3-	-	-	-2.23 Å²

Refinement step

Cycle: 1 / Resolution: 2.4→45.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11527	0	60	870	12457

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	11900
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	11107
X-RAY DIFFRACTION	r_angle_refined_deg	1.874	1.946	16236
X-RAY DIFFRACTION	r_angle_other_deg	1.063	3	25458
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.271	5	1464
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.871	23.14	586
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.237	15	1822
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.564	15	116
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1768
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13618
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2826
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	0.76	1.574	5858
X-RAY DIFFRACTION	r_mcbond_other	0.747	1.566	5849
X-RAY DIFFRACTION	r_mcangle_it	1.31	2.348	7310
X-RAY DIFFRACTION	r_mcangle_other	1.31	2.348	7311
X-RAY DIFFRACTION	r_scbond_it	0.787	1.664	6042
X-RAY DIFFRACTION	r_scbond_other	0.786	1.664	6042
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.334	2.463	8925
X-RAY DIFFRACTION	r_long_range_B_refined	6.036	13.539	13940
X-RAY DIFFRACTION	r_long_range_B_other	6.036	13.538	13940
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.462 Å / R_factor R_free error: 0.253

	R_factor	Num. reflection	% reflection
R_free	0.326	234	5 %
R_work	0.299	4428	-
obs	-	-	96.76 %

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	4.0509	-0.9222	-1.844	0.4871	0.2758	0.9163	0.2487	0.2512	0.3302	-0.1127	-0.0957	-0.0652	-0.0926	-0.1154	-0.153	0.249	0.0092	0.0084	0.2599	-0.0006	0.2616	29.1524	108.5141	81.1778
2	0.7936	1.161	-0.9848	3.3829	0.1333	4.3779	-0.0286	-0.0838	0.0896	-0.138	0.0266	-0.2838	-0.223	0.2059	0.002	0.2168	-0.014	-0.0057	0.2266	-0.0214	0.271	49.967	105.6158	87.6128
3	0.5489	-0.1911	-0.1691	0.8299	0.0421	0.2061	-0.0118	-0.0268	0.14	0.1125	0.0573	-0.0655	-0.0501	-0.0037	-0.0455	0.2618	-0.0122	-0.0102	0.2602	-0.0293	0.2056	39.558	99.9829	89.3412
4	0.8426	0.5147	0.899	1.3644	1.2275	1.4233	-0.0751	-0.0221	-0.0308	0.1032	0.0379	0.1252	-0.0121	-0.0688	0.0372	0.2556	-0.0105	0.0567	0.2939	0.0334	0.1903	9.4466	98.0356	90.3182
5	0.2921	-0.0622	-0.9013	0.6265	-0.1044	3.0919	-0.0136	0.0177	-0.0026	-0.0176	-0.0334	0.0304	-0.1174	0.0351	0.0471	0.2274	0.0087	0.0098	0.2728	-0.0095	0.2475	5.2122	102.1343	82.0332
6	0.4084	-0.2621	-0.1011	0.1896	0.0121	0.2282	-0.0231	-0.0051	-0.0151	0.0327	-0.0016	0.0356	0.0169	-0.0541	0.0247	0.2488	-0.0139	0.0283	0.2665	-0.0109	0.1861	22.4597	82.9755	86.8535
7	1.7252	-2.0236	-1.2481	3.4619	0.5414	1.8498	-0.1126	-0.106	-0.2548	0.1002	-0.0932	0.1301	0.112	0.058	0.2059	0.2856	-0.0724	0.0673	0.3121	0.065	0.2254	28.3531	55.6216	89.0736
8	0.0987	0.053	-0.1595	0.2989	0.1109	0.6064	-0.0364	0.0437	-0.0449	0.0143	-0.0115	0.0472	-0.0038	-0.0307	0.0479	0.2233	-0.0078	0.0229	0.2727	-0.0214	0.1955	33.4669	67.0261	72.0053
9	2.2468	-0.7977	-1.9679	1.0766	1.0818	2.9776	-0.0633	0.044	-0.0302	-0.045	-0.029	0.0296	0.1482	-0.0704	0.0923	0.2123	-0.0404	-0.0064	0.2701	-0.0664	0.2487	24.7421	56.0764	59.4124
10	1.7773	3.2986	-3.7881	6.1421	-7.0197	8.0928	0.1001	-0.3205	-0.0865	0.0373	-0.4525	-0.1003	-0.0408	0.6705	0.3524	0.2366	0.0599	0.0059	0.3831	0.0198	0.393	37.0624	48.1727	51.2231
11	2.7335	-0.0658	-0.5243	0.1968	-0.0845	0.155	-0.0001	0.1761	0.1177	-0.0651	-0.009	-0.0017	0.024	-0.0494	0.0092	0.2574	0.0015	0.0094	0.2538	-0.0094	0.2281	29.7607	61.2489	49.7159
12	0.1298	-0.1785	-0.0948	0.6669	0.3694	0.5896	0.0283	0.0409	0.0825	-0.0588	-0.0131	-0.0228	-0.0194	0.0038	-0.0152	0.2266	0.0144	0.0249	0.2701	0.0157	0.2159	42.1266	84.7086	59.2071
13	1.5716	-0.2873	-0.4292	2.0969	0.6505	2.2543	0.7641	-0.4275	0.3189	-0.5874	0.0717	-0.549	-0.2945	-0.1799	-0.8358	0.4236	-0.1835	0.2447	0.1576	0.0219	0.4065	78.8154	68.012	35.039
14	2.7131	-0.1388	-1.17	0.5318	0.3455	0.6823	0.1285	0.1656	0.262	-0.1723	-0.0563	-0.0785	-0.119	-0.1105	-0.0722	0.2611	0.0031	0.0879	0.2366	0.0621	0.2544	67.4116	69.1097	40.854
15	2.0578	0.5103	-1.1075	0.6943	-0.3954	0.6283	0.1117	0.2017	0.0911	-0.1431	-0.1011	-0.134	-0.0215	-0.1143	-0.0106	0.2529	0.0081	0.1399	0.2999	0.0536	0.2405	79.3851	60.5903	30.4159
16	0.6947	-0.4913	-0.1533	0.4379	0.0312	0.3617	0.0751	0.0351	0.0103	-0.0673	-0.0142	-0.1252	0.0298	0.0063	-0.0609	0.22	-0.0162	0.0457	0.2553	-0.0231	0.2619	80.9249	47.8709	42.947
17	1.4131	-0.265	-0.7186	0.5261	-0.0192	0.6788	-0.0108	-0.0063	0.0003	0.0367	0.0213	-0.1587	0.0529	-0.017	-0.0105	0.1859	-0.0143	0.0043	0.2625	-0.0335	0.2862	88.4508	39.8421	53.6009
18	0.272	-0.0203	-0.011	0.5181	0.006	0.3613	0.0164	-0.013	-0.0229	0.0079	-0.0142	-0.074	0.0391	-0.0372	-0.0023	0.2037	0.001	0.0331	0.2701	-0.0255	0.2203	67.8504	45.3304	50.5421
19	2.4781	-0.6432	-0.648	2.0667	0.5126	0.9435	0.0197	-0.0355	-0.154	-0.0171	-0.005	0.2964	0.1317	-0.0007	-0.0147	0.2396	-0.0205	0.0043	0.2595	-0.0101	0.2015	50.9147	36.3697	61.9954
20	0.0291	-0.0492	-0.1258	0.6233	0.1443	0.5734	-0.0225	0.0021	-0.0071	0.0612	-0.0039	-0.0876	0.0376	-0.044	0.0264	0.2263	-0.0174	0.0176	0.2644	-0.0158	0.2025	57.5617	54.5704	70.0121
21	1.01	-1.174	-0.9565	2.0625	1.2413	1.6797	-0.084	-0.1231	-0.0888	0.1894	-0.0551	-0.0237	0.1737	0.1309	0.139	0.3243	0.0149	-0.0045	0.2671	0.0143	0.1765	58.809	48.6959	87.2054
22	4.3427	-4.0175	-1.2164	3.7283	1.1272	0.3411	0.2098	0.1825	0.0496	-0.2262	-0.1924	-0.0803	-0.0624	-0.0575	-0.0173	0.2902	0.0219	-0.015	0.2904	0.0127	0.2373	47.5798	58.8836	96.5036
23	0.2368	-0.126	0.0172	0.7578	0.2912	0.7653	-0.0952	-0.0399	-0.0185	0.163	-0.0059	-0.1203	-0.0216	0.0974	0.1011	0.2258	-0.0161	-0.0256	0.2755	-0.0325	0.2299	65.4492	65.5591	83.7462
24	0.4849	-0.2134	-0.3413	0.3118	0.3915	0.6973	0.0265	0.0659	0.1434	-0.0259	0.0446	-0.2015	-0.0615	-0.0259	-0.0711	0.202	-0.02	0.0295	0.2604	-0.0344	0.3097	69.6013	74.9865	64.5387

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 27
3	X-RAY DIFFRACTION	3	A	28 - 152
4	X-RAY DIFFRACTION	4	A	153 - 185
5	X-RAY DIFFRACTION	5	A	186 - 203
6	X-RAY DIFFRACTION	6	A	204 - 412
7	X-RAY DIFFRACTION	7	A	413 - 438
8	X-RAY DIFFRACTION	8	A	439 - 563
9	X-RAY DIFFRACTION	9	A	564 - 600
10	X-RAY DIFFRACTION	10	A	601 - 606
11	X-RAY DIFFRACTION	11	A	607 - 622
12	X-RAY DIFFRACTION	12	A	623 - 731
13	X-RAY DIFFRACTION	13	B	1 - 26
14	X-RAY DIFFRACTION	14	B	27 - 60
15	X-RAY DIFFRACTION	15	B	61 - 118
16	X-RAY DIFFRACTION	16	B	119 - 192
17	X-RAY DIFFRACTION	17	B	193 - 257
18	X-RAY DIFFRACTION	18	B	258 - 408
19	X-RAY DIFFRACTION	19	B	409 - 446
20	X-RAY DIFFRACTION	20	B	447 - 563
21	X-RAY DIFFRACTION	21	B	564 - 598
22	X-RAY DIFFRACTION	22	B	599 - 607
23	X-RAY DIFFRACTION	23	B	608 - 645
24	X-RAY DIFFRACTION	24	B	646 - 731

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