PDB-5anh: CRYSTAL STRUCTURE OF LACCASE FROM BASIDIOMYCETE PM1 (CECT 2971)

ID or keywords:

Entry

Database: PDB / ID: 5anh

Title

CRYSTAL STRUCTURE OF LACCASE FROM BASIDIOMYCETE PM1 (CECT 2971)

Components

LACCASE

Keywords

OXIDOREDUCTASE / LACCASE / LIGNIN DEGRADATION

Function / homology

Function and homology information

hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding
Similarity search - Function

Biological species

BASIDIOMYCETE PM1 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.492 Å

Authors

Medrano, F.J. / Romero, A.

Citation

Journal: Catal.Sci..Technol / Year: 2016
Title: Re-Designing the Substrate Binding Pocket of Laccase for Enhanced Oxidation of Sinapic Acid
Authors: Pardo, I. / Santiago, G. / Gentili, P. / Lucas, F. / Monza, E. / Medrano, F.J. / Romero, A. / Galli, C. / Martinez, A.T. / Guallar, V. / Camarero, S.

History

Deposition	Sep 7, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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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Download

PDBx/mmCIF format	5anh.cif.gz	571.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5anh.ent.gz	474.8 KB	Display	PDB format
PDBx/mmJSON format	5anh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5anh_validation.pdf.gz	462.3 KB	Display	wwPDB validaton report
Full document	5anh_full_validation.pdf.gz	493 KB	Display
Data in XML	5anh_validation.xml.gz	59.3 KB	Display
Data in CIF	5anh_validation.cif.gz	82.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/an/5anh ftp://data.pdbj.org/pub/pdb/validation_reports/an/5anh	HTTPS FTP

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Related structure data

Related structure data	2hrgS S: Starting model for refinement
Similar structure data	1ahj-4 5mid-d 6rii-d 1bfn-d 3a8l-d 3x28-d 1ahj-2 2qdy-d 3t6v-1 3t6w-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2hrgS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LACCASE

B: LACCASE

C: LACCASE

hetero molecules

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

1

A: LACCASE

hetero molecules

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

2

B: LACCASE

hetero molecules

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

3

C: LACCASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.440, 175.660, 103.700
Angle α, β, γ (deg.)	90.00, 104.16, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-1498- SO4

#1: Protein	LACCASE Mass: 53274.855 Da / Num. of mol.: 3 / Fragment: UNP RESIUDES 22-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BASIDIOMYCETE PM1 (fungus) / Description: CECT 2971 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q12571, laccase
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.8 Å³/Da / Density % sol: 56.11 % / Description: NONE
Crystal grow	Details: 0.1 M TRIS-HCL PH 8.5, 1.6 M AMMONIUM SULFATE, 1.5 M LITHIUM SULFATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97908 Å / Relative weight: 1
Reflection	Resolution: 2.49→50 Å / Num. obs: 59209 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.97 % / B_iso Wilson estimate: 33.43 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 8.82
Reflection shell	Resolution: 2.49→2.64 Å / Redundancy: 2.91 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2.07 / % possible all: 89

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENRY 2HRG

2hrg

Resolution: 2.492→49.18 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 31.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2729	2963	5 %
R_work	0.1925	-	-
obs	0.1966	59184	96.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.492→49.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11295	0	37	537	11869

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11738
X-RAY DIFFRACTION	f_angle_d	1.177	16122
X-RAY DIFFRACTION	f_dihedral_angle_d	13.783	4056
X-RAY DIFFRACTION	f_chiral_restr	0.074	1824
X-RAY DIFFRACTION	f_plane_restr	0.006	2136

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 (%)
2.4924-2.5333	0.4585	97	0.3896	1882	X-RAY DIFFRACTION	69
2.5333-2.577	0.4152	143	0.3425	2702	X-RAY DIFFRACTION	98
2.577-2.6238	0.4006	142	0.3177	2690	X-RAY DIFFRACTION	98
2.6238-2.6743	0.4432	144	0.2972	2714	X-RAY DIFFRACTION	98
2.6743-2.7289	0.3675	141	0.2823	2715	X-RAY DIFFRACTION	98
2.7289-2.7882	0.3626	141	0.2644	2618	X-RAY DIFFRACTION	96
2.7882-2.8531	0.3564	141	0.2494	2701	X-RAY DIFFRACTION	98
2.8531-2.9244	0.3654	146	0.2308	2757	X-RAY DIFFRACTION	99
2.9244-3.0035	0.3186	146	0.2289	2774	X-RAY DIFFRACTION	100
3.0035-3.0918	0.3272	143	0.2191	2737	X-RAY DIFFRACTION	99
3.0918-3.1916	0.3047	146	0.2069	2736	X-RAY DIFFRACTION	99
3.1916-3.3057	0.2876	143	0.2035	2732	X-RAY DIFFRACTION	99
3.3057-3.438	0.297	143	0.1949	2703	X-RAY DIFFRACTION	98
3.438-3.5944	0.2732	145	0.1748	2734	X-RAY DIFFRACTION	98
3.5944-3.7838	0.2471	144	0.1605	2749	X-RAY DIFFRACTION	99
3.7838-4.0208	0.227	140	0.1486	2698	X-RAY DIFFRACTION	98
4.0208-4.3311	0.192	143	0.1384	2711	X-RAY DIFFRACTION	97
4.3311-4.7666	0.1935	139	0.1284	2673	X-RAY DIFFRACTION	97
4.7666-5.4556	0.1917	147	0.142	2751	X-RAY DIFFRACTION	98
5.4556-6.8705	0.2435	144	0.1755	2681	X-RAY DIFFRACTION	96
6.8705-49.1891	0.2267	145	0.1841	2763	X-RAY DIFFRACTION	97

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	0.0734	-0.0285	-0.1383	0.1676	0.071	0.1843	-0.0098	0.3769	0.0948	-0.3385	-0.0765	-0.0695	-0.302	0.135	0.0036	0.1585	-0.0172	-0.0245	0.2506	0.0035	0.188	33.5687	14.143	14.8985
2	0.2958	0.2469	-0.2635	0.1413	-0.2358	0.2453	-0.0981	0.1406	0.1079	-0.047	0.1482	0.1661	0.0206	0.039	-0.0018	0.1466	-0.0254	-0.0131	0.1923	0.021	0.121	21.1486	19.6708	20.2595
3	0.3425	-0.0751	-0.2691	0.1738	-0.0575	0.8995	-0.0268	0.0668	0.0767	0.0706	0.0582	-0.0272	-0	-0.3029	0.6661	0.1168	0.0029	0.009	0.2469	-0.0463	0.105	30.6921	6.9804	25.3588
4	0.4082	-0.0895	-0.4379	0.4913	0.0685	0.3171	-0.0071	-0.1101	-0.1011	0.1429	-0.089	-0.0332	0.0693	0.0273	-0.1227	0.0664	-0.0202	-0.029	0.1182	0.0248	0.0879	35.1446	3.5945	35.1823
5	0.3025	0.1112	0.0904	0.2168	0.0407	0.5907	-0.0049	-0.1366	-0.0656	-0.1115	0.0399	0.1636	-0.2643	-0.0427	0.0193	0.1387	-0.0948	0.0672	0.1987	-0.061	0.2815	6.099	6.3475	34.8647
6	0.1202	-0.0112	-0.0452	0.0037	0.0504	0.1262	-0.183	0.2287	-0.0125	0.0637	0.1457	0.0832	0.2583	-0.3718	-0.0003	0.2259	-0.0772	-0.0033	0.3908	0.0777	0.3672	0.1045	13.6798	19.7794
7	0.0901	-0.0245	-0.2083	0.0745	0.0555	0.3038	0.0272	0.0014	0.095	0.033	-0.0381	0.1249	0.1329	-0.1293	0.0009	0.1265	-0.0316	0.002	0.2716	-0.0218	0.2422	9.7573	6.4359	33.7514
8	0.2198	-0.0032	0.1288	0.1998	-0.1383	0.2386	-0.0115	0.2222	0.0347	-0.0115	-0.1408	-0.0875	0.0226	-0.3383	-0.0109	0.2119	0.0312	-0.0142	0.3863	0.0619	0.298	10.1815	16.7481	13.7561
9	-0.0018	-0.0253	-0.0104	-0.0127	0.0227	0.0502	-0.1334	0.2219	-0.1883	0.011	0.0506	-0.0938	0.2121	0.0769	-0	0.3201	-0.0157	0.0354	0.1957	-0.0137	0.1955	3.6057	-50.175	14.8455
10	0.262	0.1557	-0.187	0.4534	0.1954	0.3203	-0.0131	0.069	-0.0312	-0.0996	0.0365	-0.2476	-0.1104	-0.0323	0.0027	0.1703	-0.0209	-0.0084	0.134	-0.0011	0.1245	14.4952	-42.489	21.0618
11	0.1875	0.1676	-0.2987	0.404	0.1786	0.4736	0.01	-0.0222	0.0436	0.0071	0.0331	0.0545	-0.082	-0.0289	0	0.1242	-0.0094	0.0009	0.0791	-0.0006	0.1289	-5.5629	-45.7297	32.9964
12	0.1629	-0.0484	-0.1597	0.1089	0.0432	0.1451	-0.023	-0.0006	0.1414	0.1483	0.0162	0.1043	-0.2127	0.1615	0	0.3484	0.0015	-0.0056	0.1576	-0.0306	0.2808	10.6134	-22.5444	34.9708
13	0.277	-0.1694	0.0002	0.16	-0.0648	0.0884	0.0161	0.0609	0.3596	-0.3195	0.1906	-0.0439	-0.29	0.1444	0.0849	0.4091	-0.2413	0.1064	-0.1648	-0.1982	0.3438	19.9204	-21.1832	14.8311
14	0.0912	-0.017	0.1456	0.0707	0.0856	0.4405	-0.1192	-0.1024	-0.0642	0.1174	0.1322	-0.1175	-0.3175	-0.1502	0.0061	0.2348	-0.0569	-0.0696	0.1254	-0.0276	0.2895	10.2293	-24.5591	34.4911
15	0.2459	0.1992	-0.0848	0.3019	0.1089	0.249	-0.156	0.1136	0.1892	-0.4338	0.0311	-0.1353	-0.2895	0.1589	-0.0768	0.405	-0.0368	0.0987	0.2803	0.0006	0.2466	17.0802	-30.6871	15.213
16	0.0349	0.022	-0.0814	0.0439	0.0507	0.1176	0.0067	0.1737	0.0601	-0.3525	-0.0625	0.2365	-0.2093	-0.1335	-0.0055	0.218	0.0387	-0.0201	0.233	-0.0156	0.2144	-37.1603	7.8634	14.8054
17	0.4722	-0.3083	0.3088	0.5305	0.0732	0.3175	0.0719	0.0933	-0.1819	-0.078	0.0438	0.0917	0.0952	0.0833	0.0017	0.164	0.0232	-0.0189	0.1516	0.0022	0.1564	-35.7583	-5.6415	20.2961
18	0.1436	-0.1345	0.06	0.1865	0.1122	0.2079	0.0323	-0.007	0.0641	0.0543	0.036	-0.1381	-0.0612	0.1288	0.0003	0.1569	0.0078	0.0008	0.1366	-0.0036	0.1497	-30.5978	12.3543	27.55
19	0.4601	-0.3027	-0.0065	0.1351	0.001	0.3364	0.0816	-0.0743	0.0397	0.007	-0.0302	-0.0378	-0.0444	0.0485	-0	0.1542	0.0084	-0.0378	0.1503	-0.0081	0.1827	-27.631	14.3223	37.621
20	0.2536	-0.0698	-0.0202	0.3936	0.3603	0.2767	-0.0584	-0.0143	-0.2418	0.1191	0.1249	-0.1592	0.1918	-0.1226	0.1525	0.136	0.0315	0.0555	0.2694	0.0449	0.2733	-16.6426	-11.9021	35.032
21	0.0153	0.063	-0.0293	0.2291	-0.222	0.2562	-0.018	0.0958	-0.1472	-0.3801	-0.2767	-0.2256	-0.0463	0.1507	-0.0557	0.3114	0.1628	0.0427	0.3648	-0.1628	0.3865	-20.2333	-20.6862	14.8502
22	0.1172	0.1793	-0.1527	0.1957	-0.1169	0.4734	0.0948	-0.2862	-0.1241	0.1529	-0.089	-0.038	-0.062	0.263	-0.0099	0.2005	0.0747	0.014	0.1758	0.0508	0.2346	-18.2331	-10.6328	34.5035
23	0.0545	-0.1009	0.0738	0.3638	-0.0104	0.5207	0.1022	0.2134	-0.1516	-0.1676	-0.3241	-0.074	0.0139	0.1935	-0.0768	0.2674	0.1189	-0.0393	0.2106	-0.0712	0.2146	-27.0408	-13.5738	15.1588

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 35 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 36 THROUGH 133 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 134 THROUGH 166 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 167 THROUGH 300 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 301 THROUGH 338 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 339 THROUGH 382 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 383 THROUGH 450 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 451 THROUGH 496 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 1 THROUGH 35 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 36 THROUGH 136 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 137 THROUGH 300 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 301 THROUGH 338 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 339 THROUGH 369 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 370 THROUGH 443 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 444 THROUGH 496 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 1 THROUGH 35 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 36 THROUGH 133 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 134 THROUGH 207 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 208 THROUGH 300 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 301 THROUGH 338 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 339 THROUGH 369 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 370 THROUGH 443 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 444 THROUGH 496 )

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi