PDB-5m8z: PCE reductive dehalogenase from S. multivorans in complex with 2,...

ID or keywords:

Entry

Database: PDB / ID: 5m8z

Title

PCE reductive dehalogenase from S. multivorans in complex with 2,3-difluorophenol

Components

Tetrachloroethene reductive dehalogenase catalytic subunit PceA

Keywords

OXIDOREDUCTASE / organohalide respiration anaerobic crystallisation cobalamin

Function / homology

Function and homology information

4 iron, 4 sulfur cluster binding / identical protein binding / metal ion binding
Similarity search - Function

Biological species

Sulfurospirillum multivorans DSM 12446 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.659 Å

Authors

Kunze, C. / Bommer, M. / Hagen, W.R. / Uksa, M. / Dobbek, H. / Schubert, T. / Diekert, G.

Funding support

Germany, 2items

Citation

Journal: Nat Commun / Year: 2017
Title: Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer.
Authors: Kunze, C. / Bommer, M. / Hagen, W.R. / Uksa, M. / Dobbek, H. / Schubert, T. / Diekert, G.

History

Deposition	Oct 30, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5m8z.cif.gz	378.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5m8z_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5m8z_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5m8z_validation.xml.gz	41.1 KB	Display
Data in CIF	5m8z_validation.cif.gz	61.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m8/5m8z ftp://data.pdbj.org/pub/pdb/validation_reports/m8/5m8z	HTTPS FTP

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Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8yC 5m90C 5m91C 5m92C 5ma0C 5ma1C 5ma2C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5m8w-d 5ma0-d 5m8y-d 5m90-d 5obi-d 5m8u-d 5m2g-d 5ma2-d 4ur2-d 5obp-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	#220 - Apr 2018 Dehalogenases similarity (12) #111 - Mar 2009 Hydrogenase similarity (6) #144 - Dec 2011 Complex I similarity (4) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (4) #22 - Oct 2001 Photosystem I similarity (4) #66 - Jun 2005 Carotenoid Oxygenase similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (4)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#220 - Apr 2018
Dehalogenases
similarity (12)
#111 - Mar 2009
Hydrogenase
similarity (6)
#144 - Dec 2011
Complex I
similarity (4)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (4)
#154 - Oct 2012
Citric Acid Cycle
similarity (4)
#22 - Oct 2001
Photosystem I
similarity (4)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (4)
#241 - Jan 2020
Twenty Years of Molecules
similarity (4)

Deposited unit

A: Tetrachloroethene reductive dehalogenase catalytic subunit PceA

B: Tetrachloroethene reductive dehalogenase catalytic subunit PceA

hetero molecules

110 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)	73.579, 73.579, 184.962
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Tetrachloroethene reductive dehalogenase catalytic subunit PceA Mass: 52164.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Sulfurospirillum multivorans DSM 12446 (bacteria) Plasmid details: DSM-12446 / References: UniProt: W6EQP0

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Non-polymers , 6 types, 764 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-BVQ / NORPSEUDO-B12 Mass: 1305.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅₇H₈₂CoN₁₆O₁₄P
#4: Chemical	ChemComp-BEN / BENZAMIDINE Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₈N₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-ZTN / 2,3-bis(fluoranyl)phenol Mass: 130.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₄F₂O
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 744 / 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: 2.5 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15 percent PEG 3350, 200 mM sodium malonate, 2 percent benzamidineHCl, and 50 mM TrisHCl, pH 7.5 under an atmosphere of 95 percent N2, 5 percent H2 and less than 10 ppm oxygen

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2014
Radiation	Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.659→47.3 Å / Num. obs: 115571 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / B_iso Wilson estimate: 20.68 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.05253 / Net I/σ(I): 21.92
Reflection shell	Resolution: 1.659→1.718 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.6218 / Mean I/σ(I) obs: 2.81 / CC_1/2: 0.824 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS	November 3, 2014	data reduction
XDS	November 3, 2014	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UQU

4uqu

Resolution: 1.659→47.257 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 15.22

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.161	5776	5.01 %	Random selection
R_work	0.1375	-	-	-
obs	0.1386	115504	99.08 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 28.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.659→47.257 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6809	0	309	744	7862

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7411
X-RAY DIFFRACTION	f_angle_d	1.027	10088
X-RAY DIFFRACTION	f_dihedral_angle_d	15.151	4413
X-RAY DIFFRACTION	f_chiral_restr	0.063	1044
X-RAY DIFFRACTION	f_plane_restr	0.006	1373

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 (%)
1.6591-1.6779	0.2596	374	0.244	7014	X-RAY DIFFRACTION	96
1.6779-1.6977	0.2404	377	0.2352	7137	X-RAY DIFFRACTION	99
1.6977-1.7184	0.2631	377	0.2182	7131	X-RAY DIFFRACTION	99
1.7184-1.7401	0.2344	383	0.2132	7239	X-RAY DIFFRACTION	99
1.7401-1.763	0.2366	381	0.2092	7167	X-RAY DIFFRACTION	99
1.763-1.7872	0.2401	381	0.2092	7229	X-RAY DIFFRACTION	99
1.7872-1.8127	0.1975	381	0.1906	7194	X-RAY DIFFRACTION	99
1.8127-1.8398	0.1995	384	0.1793	7187	X-RAY DIFFRACTION	99
1.8398-1.8685	0.1866	376	0.1719	7176	X-RAY DIFFRACTION	99
1.8685-1.8992	0.1849	378	0.1593	7158	X-RAY DIFFRACTION	99
1.8992-1.9319	0.1772	386	0.1566	7312	X-RAY DIFFRACTION	99
1.9319-1.9671	0.177	370	0.1491	7091	X-RAY DIFFRACTION	99
1.9671-2.0049	0.163	382	0.1491	7239	X-RAY DIFFRACTION	99
2.0049-2.0458	0.1726	379	0.1448	7259	X-RAY DIFFRACTION	99
2.0458-2.0903	0.1728	376	0.1422	7157	X-RAY DIFFRACTION	99
2.0903-2.1389	0.1649	379	0.139	7195	X-RAY DIFFRACTION	99
2.1389-2.1924	0.1701	381	0.1301	7262	X-RAY DIFFRACTION	99
2.1924-2.2517	0.1531	382	0.1287	7269	X-RAY DIFFRACTION	99
2.2517-2.3179	0.1508	380	0.1284	7223	X-RAY DIFFRACTION	99
2.3179-2.3928	0.1599	375	0.131	7175	X-RAY DIFFRACTION	99
2.3928-2.4783	0.1553	384	0.1335	7257	X-RAY DIFFRACTION	99
2.4783-2.5775	0.173	377	0.1319	7208	X-RAY DIFFRACTION	99
2.5775-2.6948	0.1664	382	0.1321	7249	X-RAY DIFFRACTION	99
2.6948-2.8368	0.1663	385	0.1324	7277	X-RAY DIFFRACTION	100
2.8368-3.0146	0.1596	378	0.1318	7194	X-RAY DIFFRACTION	100
3.0146-3.2473	0.1393	381	0.1263	7205	X-RAY DIFFRACTION	100
3.2473-3.5739	0.1516	384	0.123	7253	X-RAY DIFFRACTION	99
3.5739-4.0909	0.1326	381	0.1154	7222	X-RAY DIFFRACTION	99
4.0909-5.153	0.1288	386	0.1145	7247	X-RAY DIFFRACTION	100
5.153-47.2761	0.1519	384	0.1359	7187	X-RAY DIFFRACTION	99

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	0.1954	0.1337	0.0558	0.3113	0.2993	0.2522	0.0555	-0.1246	0.003	0.0427	0.0019	0.1049	-0.0276	-0.1879	0.0002	0.2022	0.0302	-0.0221	0.2397	-0.0371	0.2078	-14.1793	-17.941	4.6732
2	0.2054	0.0511	0.1543	0.5747	0.4132	0.6472	-0.0229	0.0277	0.0212	-0.1282	-0.0044	0.0318	-0.1176	-0.0801	0.0005	0.1976	-0.0064	-0.0283	0.1524	-0.0061	0.166	-7.8821	-23.6248	-16.0769
3	0.1222	-0.0666	-0.0866	0.6243	0.1565	0.2937	0.0103	0.0023	0.0125	-0.1162	-0.0482	0.0977	-0.1231	-0.1429	0	0.1781	0.0061	-0.0579	0.2072	-0.0222	0.1699	-16.3458	-23.0163	-16.0932
4	0.1314	0.0656	0.0403	0.4369	0.1003	0.5225	0.0153	-0.0434	0.0183	-0.0033	-0.0439	0.0379	-0.0721	-0.1165	-0	0.1719	-0.004	-0.0264	0.1605	-0.0254	0.1588	-9.9617	-22.9651	-3.8009
5	0.0643	0.071	0.0813	0.1436	0.1499	0.14	0.033	0.0021	0.107	-0.0974	-0.0394	0.0484	-0.3916	-0.1047	-0.0002	0.342	0.0427	-0.042	0.1529	-0.0299	0.2113	-9.5946	-3.7718	-7.1615
6	0.2281	0.0396	-0.0593	0.0845	0.0528	0.2484	-0.0671	-0.1294	0.0425	-0.0441	-0.0394	-0.0064	-0.1292	0.2165	0.0051	0.2056	-0.0104	-0.0213	0.1669	-0.0126	0.1561	2.1277	-16.066	5.1625
7	0.0061	0.0456	-0.0014	0.0996	0.158	0.1578	0.0464	-0.2342	-0.0074	0.1773	0.01	-0.087	0.0283	0.1738	0.0173	0.2247	-0.0668	-0.0262	0.2327	-0.0514	0.2178	4.022	-25.9389	3.4507
8	0.1621	-0.0369	-0.1072	0.2881	0.0978	0.5795	0.0689	-0.0302	-0.0965	0.0856	0.0773	-0.2341	0.4065	0.1063	0.0829	0.2881	0.053	-0.0513	0.2097	-0.0796	0.314	8.7305	-56.6112	-19.8081
9	0.2172	-0.0059	-0.0394	0.1038	0.1306	0.1244	0.0581	-0.0499	-0.0122	0.1168	-0.0426	0.0216	0.1776	-0.0843	-0.0186	0.274	-0.0922	-0.0307	0.154	0.0079	0.1605	-14.94	-54.5582	-8.8579
10	0.0456	-0.0169	-0.0083	0.2689	0.3505	0.5386	0.0023	0.0553	-0.0259	-0.1362	0.1052	-0.1438	-0.0418	0.0861	0	0.2096	-0.0313	0.0042	0.1715	-0.0434	0.2086	7.5649	-35.6424	-25.0156
11	0.2692	0.129	-0.0263	0.6242	0.3222	0.228	0.0053	0.0757	-0.054	-0.0871	0.1187	-0.1392	0.039	0.0346	0.0001	0.2346	-0.0399	-0.006	0.1964	-0.0341	0.1979	2.7882	-45.8268	-27.4077
12	0.3163	0.2552	0.1249	0.648	0.3197	0.5919	0.0482	0.0098	-0.0765	0.0403	0.0945	-0.2033	0.1378	0.1336	0.5394	0.1958	0.0229	-0.0485	0.1597	-0.0501	0.2417	10.0792	-45.8575	-14.8893
13	0.2698	0.0012	-0.1027	0.1712	-0.1564	0.9965	0.1543	0.0105	-0.3635	0.2106	0.1147	-0.1785	0.7071	-0.2279	0.3262	0.43	0.1035	-0.1513	-0.0182	-0.1173	0.3904	6.5192	-64.9714	-16.0629
14	0.0081	0.0156	0.0269	0.0463	0.0479	0.0862	0.1438	-0.1212	-0.0636	0.3029	-0.0269	-0.0913	0.2628	-0.0677	0.005	0.372	-0.0397	-0.0885	0.1734	0.0084	0.2188	-1.5122	-51.1821	-0.1212
15	0.0362	-0.0524	-0.0093	0.1062	0.0802	0.0915	-0.0227	-0.0458	-0.091	0.1507	0.0948	-0.1527	0.0582	0.1691	0.0017	0.201	-0.0037	-0.0674	0.229	-0.0303	0.2344	12.0089	-35.0218	-3.0122

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 176 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 177 through 235 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 236 through 338 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 339 through 379 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 380 through 404 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 405 through 462 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 7 through 52 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 53 through 98 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 99 through 176 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 177 through 235 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 236 through 338 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 339 through 379 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 380 through 441 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 442 through 461 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 764 molecules

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