PDB-3ta4: Small laccase from Amycolatopsis sp. ATCC 39116 complexed with 1-...

ID or keywords:

Entry

Database: PDB / ID: 3ta4

Title

Small laccase from Amycolatopsis sp. ATCC 39116 complexed with 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-dihydroxypropane

Components

small laccase, multi-copper oxidase

Keywords

OXIDOREDUCTASE / 2-domain copper oxidase /

secreted

Function / homology

Function and homology information

hydroquinone:oxygen oxidoreductase activity /

laccase / copper ion binding
Similarity search - Function

Biological species

Amycolatopsis sp. ATCC 39116 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Lukk, T. / Majumdar, S. / Gerlt, J.A. / Nair, S.K.

Citation

Journal: Biochemistry / Year: 2014
Title: Roles of small laccases from Streptomyces in lignin degradation.
Authors: Majumdar, S. / Lukk, T. / Solbiati, J.O. / Bauer, S. / Nair, S.K. / Cronan, J.E. / Gerlt, J.A.

History

Deposition	Aug 3, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 11, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	Oct 11, 2017	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ta4.cif.gz	181.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3ta4.ent.gz	143.5 KB	Display	PDB format
PDBx/mmJSON format	3ta4.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ta/3ta4 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/3ta4	HTTPS FTP

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Related structure data

Related structure data	3t9wC 3tasC 3tbbC 3tbcC C: citing same article (ref.)
Similar structure data	5ue6-2 3kw8-1 2b3y-2 6qpt-2 2xij-d 5ue6-3 6smp-1 6qpu-2 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

Deposited unit

F: small laccase, multi-copper oxidase

D: small laccase, multi-copper oxidase

E: small laccase, multi-copper oxidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	84.420, 115.260, 163.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Details

Determined via gel filtration chromatography.

#1: Protein	small laccase, multi-copper oxidase Mass: 33249.148 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis sp. ATCC 39116 (bacteria) Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J9PBQ8*PLUS, laccase
#2: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-TO2 / (1R,2S)-1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol Mass: 334.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₂₂O₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.99 Å³/Da / Density % sol: 38.31 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: The protein concentration was 20 mg/mL buffered with 20 mM Tris-HCl; precipitate contained 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.9

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 29, 2010

Radiation

Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.35→20 Å / Num. all: 33627 / Num. obs: 33545 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 36.34 Å² / R_merge(I) obs: 0.116 / Net I/σ(I): 20.65

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.35-2.41	0.812	2.71	20984	2456	1	99.8
2.41-2.48	0.666	3.95	27230	2380	1	100
2.48-2.55	0.521	5.17	27435	2351	1	100
2.55-2.63	0.487	5.65	26859	2251	1	100
2.63-2.71	0.407	6.84	26414	2181	1	100
2.71-2.81	0.324	8.6	26131	2127	1	100
2.81-2.91	0.256	10.74	25356	2051	1	100
2.91-3.03	0.198	13.62	24563	1986	1	100
3.03-3.17	0.155	17.09	23533	1893	1	100
3.17-3.32	0.127	20.71	22517	1817	1	100
3.32-3.5	0.098	26.55	21470	1747	1	100
3.5-3.72	0.073	33.26	20184	1644	1	100
3.72-3.97	0.065	37.54	19078	1563	1	100
3.97-4.29	0.052	43.66	17460	1427	1	100
4.29-4.7	0.047	48.77	16401	1348	1	99.9
4.7-5.25	0.045	49.07	14823	1222	1	100
5.25-6.07	0.047	45.92	13062	1081	1	100
6.07-7.43	0.046	45.78	10964	919	1	100
7.43-10.51	0.037	52.51	8572	739	1	100
10.51-20	0.03	59.16	3755	362	1	82.8

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_764	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→19.799 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8437 / SU ML: 0.64 / σ(F): 2 / Phase error: 22.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.238	1677	5 %
R_work	0.1762	-	-
obs	0.1794	33510	99.97 %
all	-	33627	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 21.194 Å² / k_sol: 0.348 e/Å³

Displacement parameters

B_iso max: 98.36 Å² / B_iso mean: 29.6505 Å² / B_iso min: 9.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.0704 Å²	-0 Å²	0 Å²
2-	-	-0.5018 Å²	0 Å²
3-	-	-	0.4314 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→19.799 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6426	0	40	265	6731

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6664
X-RAY DIFFRACTION	f_angle_d	1.408	9050
X-RAY DIFFRACTION	f_chiral_restr	0.111	920
X-RAY DIFFRACTION	f_plane_restr	0.008	1195
X-RAY DIFFRACTION	f_dihedral_angle_d	14.306	2365

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.3501-2.4191	0.3175	138	0.2386	2606	2744
2.4191-2.4971	0.3279	137	0.2235	2619	2756
2.4971-2.5861	0.3078	138	0.2136	2620	2758
2.5861-2.6894	0.2871	138	0.204	2617	2755
2.6894-2.8115	0.3047	139	0.1991	2644	2783
2.8115-2.9593	0.2812	139	0.1935	2631	2770
2.9593-3.144	0.2408	138	0.1849	2642	2780
3.144-3.3857	0.2359	140	0.1829	2658	2798
3.3857-3.7243	0.2352	140	0.1728	2646	2786
3.7243-4.2586	0.1914	140	0.1564	2666	2806
4.2586-5.3478	0.1797	142	0.1302	2695	2837
5.3478-19.8001	0.2227	148	0.1698	2789	2937

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	0.529	0.2119	0.1471	0.5943	0.2176	0.438	0.2258	0.0805	-0.1018	0.1682	-0.0237	0.3825	-0.1012	-0.171	0.3147	0.1691	0.0806	0.1073	0.4037	-0.0377	0.3396	-40.3533	-25.0914	34.9972
2	0.1343	0.0914	-0.1196	0.4119	0.0852	0.53	0.0001	-0.0467	0.0418	0.0392	0.047	0.1264	-0.1437	-0.0629	-0.0005	0.1141	0.0088	0.0319	0.1638	-0.0153	0.1601	-26.6638	-24.2387	37.0217
3	0.3497	0.0219	-0.0593	1.0074	0.634	0.4133	-0.0744	-0.0177	-0.0485	0.1176	-0.0161	0.2046	0.1653	-0.0967	-0.0479	0.1169	-0.0231	0.0426	0.1598	0.0014	0.1203	-25.2087	-42.4844	35.0813
4	0.1752	0.295	0.118	0.5585	0.0642	0.1777	-0.156	-0.0953	0.2043	-0.125	-0.0369	0.0663	0.0214	-0.0293	-0.0041	0.1764	-0.0159	0.0208	0.2134	-0.0134	0.1531	-19.1201	-43.5244	21.9937
5	0.4955	-0.2885	-0.4082	0.6559	0.2426	0.3216	-0.0141	-0.1139	-0.0865	0.1989	-0.016	0.0535	0.0813	0.0574	-0.0003	0.1637	0.0021	0.0372	0.1735	0.0259	0.1272	-20.603	-52.0976	34.5459
6	0.237	0.2468	-0.2042	0.647	-0.1508	0.1896	0.2315	-0.1394	0.2722	-0.1284	-0.0364	-0.1123	-0.382	0.0315	0.0276	0.2775	-0.0118	0.0263	0.2773	-0.0107	0.2185	6.626	-13.0527	13.0953
7	0.4871	0.2013	0.0884	0.3484	0.2721	0.6249	0.007	0.0041	-0.0205	-0.0587	0.0173	-0.1067	-0.1006	0.0497	0.0007	0.1617	-0.0131	0.0208	0.1428	0.0295	0.1348	3.1521	-24.8219	8.2321
8	0.2655	-0.0939	-0.0512	0.0474	0.003	0.0201	0.034	-0.2621	0.0827	0.1187	0.0971	-0.1085	-0.2933	0.0896	0.0006	0.2438	-0.0199	0.0055	0.32	-0.012	0.1806	-3.7022	-16.4207	27.008
9	0.5254	-0.071	0.1298	0.6971	0.505	0.4193	0.041	-0.0015	-0.0264	-0.0226	-0.0601	0.1398	-0.0635	-0.0264	-0.0001	0.1625	-0.0066	0.0138	0.1463	0.0125	0.1385	-16.0552	-22.794	20.9612
10	0.193	0.2406	0.1548	0.3431	0.1157	0.2217	-0.0698	-0.1157	0.104	0.119	0.0037	-0.2229	-0.1566	0.1221	-0.0004	0.2447	0.0287	-0.0098	0.2245	-0.0344	0.1409	-14.1005	-11.5508	31.3853
11	0.0424	0.1309	-0.0673	0.4937	-0.4052	0.3377	-0.0468	0.2242	0.0612	-0.0385	-0.0005	-0.1048	0.2442	0.1176	0	0.2123	0.019	0.0104	0.2493	0.0036	0.2421	0.9157	-64.3141	20.6745
12	0.1378	0.0727	0.0811	0.6083	-0.0576	0.6674	0.0996	-0.0545	-0.2005	-0.0571	-0.0158	0.0214	0.2808	-0.1244	0.0008	0.1964	0.0013	0.032	0.1869	0.0087	0.221	-12.9506	-63.0043	23.8016
13	0.4077	0.0214	0.2336	0.2758	-0.0465	0.1775	-0.074	-0.1315	-0.1193	-0.0354	0.0441	0.0049	-0.092	-0.1257	-0.0001	0.196	0.01	0.0146	0.1969	0.0033	0.1718	-9.2297	-54.1179	19.9432
14	0.1726	0.0177	0.0153	0.3615	-0.2662	0.207	-0.0198	0.0726	0.0312	-0.0041	-0.0163	-0.1545	-0.0377	0.0079	-0	0.1387	-0.0078	0.0175	0.1534	-0.0028	0.1683	3.05	-45.0854	15.7266
15	0.3134	0.0046	0.0738	0.4487	-0.1371	0.0556	-0.0226	-0.0061	0.2004	0.0493	-0.0928	-0.0624	0.0649	-0.0413	-0.0063	0.1676	-0.0149	0.0089	0.1556	-0.0428	0.1427	-13.2362	-37.644	8.7826
16	0.2505	-0.3404	-0.0262	0.5759	-0.1454	0.2119	-0.0168	0.1032	-0.0481	0.0197	-0.0411	-0.169	0.1055	0.0103	-0	0.1968	-0.0167	0.0372	0.205	0.0046	0.1988	5.2248	-40.592	11.7711

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'F' and (resseq 28:50)	F
2	X-RAY DIFFRACTION	2	chain 'F' and (resseq 51:164)	F
3	X-RAY DIFFRACTION	3	chain 'F' and (resseq 165:217)	F
4	X-RAY DIFFRACTION	4	chain 'F' and (resseq 218:253)	F
5	X-RAY DIFFRACTION	5	chain 'F' and (resseq 254:309)	F
6	X-RAY DIFFRACTION	6	chain 'D' and (resseq 37:69)	D
7	X-RAY DIFFRACTION	7	chain 'D' and (resseq 70:179)	D
8	X-RAY DIFFRACTION	8	chain 'D' and (resseq 180:201)	D
9	X-RAY DIFFRACTION	9	chain 'D' and (resseq 202:279)	D
10	X-RAY DIFFRACTION	10	chain 'D' and (resseq 280:309)	D
11	X-RAY DIFFRACTION	11	chain 'E' and (resseq 37:69)	E
12	X-RAY DIFFRACTION	12	chain 'E' and (resseq 70:133)	E
13	X-RAY DIFFRACTION	13	chain 'E' and (resseq 134:179)	E
14	X-RAY DIFFRACTION	14	chain 'E' and (resseq 180:231)	E
15	X-RAY DIFFRACTION	15	chain 'E' and (resseq 232:253)	E
16	X-RAY DIFFRACTION	16	chain 'E' and (resseq 254:303)	E

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