PDB-5m8y: PCE reductive dehalogenase from S. multivorans in complex with 3-...

ID or keywords:

Entry

Database: PDB / ID: 5m8y

Title

PCE reductive dehalogenase from S. multivorans in complex with 3-chlorophenol

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: 1.857 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 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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5m8y.cif.gz	375.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5m8y.ent.gz	304.1 KB	Display	PDB format
PDBx/mmJSON format	5m8y.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5m8y_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5m8y_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5m8y_validation.xml.gz	40.7 KB	Display
Data in CIF	5m8y_validation.cif.gz	61.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m8/5m8y ftp://data.pdbj.org/pub/pdb/validation_reports/m8/5m8y	HTTPS FTP

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Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8zC 5m90C 5m91C 5m92C 5ma0C 5ma1C 5ma2C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5m8z-d 5ma0-d 5m90-d 5m8w-d 5m2g-d 5maa-d 4ur2-d 5m8u-d 5obi-d 4ur3-3 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 (11) #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 (11)
#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

109 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)	73.783, 73.783, 185.233
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 , 5 types, 779 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-3CH / 3-CHLOROPHENOL Mass: 128.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅ClO
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 763 / 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: 1.9 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: 1.9 Å / Relative weight: 1
Reflection	Resolution: 1.857→47.4 Å / Num. obs: 80964 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / B_iso Wilson estimate: 24.83 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.0538 / Net I/σ(I): 29.08
Reflection shell	Resolution: 1.857→1.924 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.3731 / Mean I/σ(I) obs: 3.27 / CC_1/2: 0.851 / % possible all: 78

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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: 1.857→47.352 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.01

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1603	4047	5 %	Random selection
R_work	0.1301	-	-	-
obs	0.1316	80946	96.95 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 29.65 Å²

Refinement step

Cycle: LAST / Resolution: 1.857→47.352 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6795	0	274	763	7832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7356
X-RAY DIFFRACTION	f_angle_d	0.918	10018
X-RAY DIFFRACTION	f_dihedral_angle_d	14.714	4393
X-RAY DIFFRACTION	f_chiral_restr	0.058	1043
X-RAY DIFFRACTION	f_plane_restr	0.006	1346

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 (%)
1.8574-1.8785	0.2708	158	0.2376	3160	X-RAY DIFFRACTION	59
1.8785-1.9006	0.2236	214	0.2088	4002	X-RAY DIFFRACTION	76
1.9006-1.9238	0.2081	232	0.1863	4407	X-RAY DIFFRACTION	85
1.9238-1.9482	0.2132	257	0.1809	4853	X-RAY DIFFRACTION	92
1.9482-1.9738	0.192	268	0.1704	5059	X-RAY DIFFRACTION	97
1.9738-2.0008	0.2016	275	0.1526	5205	X-RAY DIFFRACTION	99
2.0008-2.0294	0.1866	270	0.1483	5149	X-RAY DIFFRACTION	100
2.0294-2.0597	0.1875	278	0.1402	5240	X-RAY DIFFRACTION	100
2.0597-2.0919	0.1641	276	0.1402	5242	X-RAY DIFFRACTION	100
2.0919-2.1262	0.1729	276	0.1381	5238	X-RAY DIFFRACTION	100
2.1262-2.1629	0.1907	270	0.132	5234	X-RAY DIFFRACTION	100
2.1629-2.2022	0.1641	270	0.1299	5138	X-RAY DIFFRACTION	100
2.2022-2.2445	0.178	273	0.1281	5213	X-RAY DIFFRACTION	100
2.2445-2.2904	0.154	279	0.1266	5288	X-RAY DIFFRACTION	100
2.2904-2.3402	0.1587	270	0.1261	5145	X-RAY DIFFRACTION	100
2.3402-2.3946	0.149	276	0.1258	5252	X-RAY DIFFRACTION	100
2.3946-2.4545	0.1696	279	0.1306	5251	X-RAY DIFFRACTION	100
2.4545-2.5208	0.1751	271	0.1209	5163	X-RAY DIFFRACTION	100
2.5208-2.595	0.1523	274	0.1277	5239	X-RAY DIFFRACTION	100
2.595-2.6788	0.169	277	0.1274	5235	X-RAY DIFFRACTION	100
2.6788-2.7745	0.1691	272	0.1252	5184	X-RAY DIFFRACTION	100
2.7745-2.8856	0.159	279	0.1303	5252	X-RAY DIFFRACTION	100
2.8856-3.0169	0.1803	272	0.1322	5170	X-RAY DIFFRACTION	100
3.0169-3.1759	0.183	276	0.1317	5296	X-RAY DIFFRACTION	100
3.1759-3.3748	0.1733	274	0.1251	5193	X-RAY DIFFRACTION	100
3.3748-3.6353	0.1276	272	0.1217	5188	X-RAY DIFFRACTION	100
3.6353-4.001	0.14	274	0.1165	5261	X-RAY DIFFRACTION	100
4.001-4.5795	0.135	274	0.1092	5214	X-RAY DIFFRACTION	100
4.5795-5.7681	0.1359	275	0.126	5208	X-RAY DIFFRACTION	100
5.7681-47.367	0.1484	275	0.1386	5194	X-RAY DIFFRACTION	100

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	0.3013	0.0689	0.1758	0.3902	0.3402	0.3035	-0.0216	-0.0768	0.0975	-0.03	-0.0037	0.0647	-0.1176	-0.1738	0.0001	0.2368	0.0319	-0.0356	0.2148	-0.0239	0.2422	-12.2303	-13.703	-4.8592
2	0.1129	-0.097	-0.0463	0.1264	-0.0161	0.1862	-0.0351	0.0192	-0.0282	-0.1968	0.0478	-0.1299	-0.1915	0.09	0.0004	0.314	-0.0682	0.0123	0.1821	-0.0116	0.2111	8.11	-14.297	-22.0168
3	0.0838	-0.0084	0.1003	0.2913	0.2912	0.3608	0.0136	-0.0157	-0.0039	0.0105	-0.0624	0.0923	0.0295	-0.1297	-0	0.2083	-0.0133	-0.0222	0.2212	-0.0264	0.2191	-17.3852	-33.143	-11.037
4	0.2102	-0.0853	0.0442	0.5801	0.1779	0.3302	-0.0157	-0.0191	0.0065	-0.0761	-0.0422	0.082	-0.1111	-0.1062	0	0.206	0.002	-0.0555	0.2313	-0.0248	0.2012	-16.4238	-23.0131	-16.0492
5	0.2	0.0239	-0.0144	0.3968	0.0864	0.6228	0.0008	-0.043	0.0116	-0.0257	-0.0352	0.0311	-0.1242	-0.0922	0	0.2118	0.0109	-0.0394	0.1648	-0.0235	0.1736	-9.9361	-17.3191	-4.6272
6	0.1227	0.1077	-0.0189	0.0568	-0.005	0.0152	-0.0631	-0.1102	0.0467	-0.0402	-0.0493	-0.0011	-0.1111	0.1503	-0.0003	0.2363	-0.0006	-0.0331	0.1991	-0.0079	0.1916	2.0334	-16.0906	5.2116
7	0.0046	0.0979	0.0272	0.0571	0.1056	0.1324	0.0451	-0.1956	-0.0012	0.1663	0.0167	-0.0761	0.0192	0.1715	0.0027	0.2538	-0.0532	-0.0322	0.2464	-0.0386	0.2276	3.9741	-25.9621	3.4765
8	0.0663	0.0129	-0.1046	0.4616	-0.0296	0.395	0.0421	-0.0358	-0.0965	0.0179	0.0521	-0.2206	0.3591	0.0987	0.0027	0.273	0.0327	-0.0397	0.2157	-0.0554	0.2855	8.7063	-56.6058	-19.8324
9	0.1005	-0.0679	-0.0764	0.1638	0.1754	0.1559	0.048	-0.0318	0.0168	0.0887	-0.0573	0.0574	0.1659	-0.0948	-0.0004	0.2931	-0.0847	-0.0337	0.1727	0.0076	0.1882	-15.0042	-54.6273	-8.9344
10	0.056	0.0382	0.0557	0.0543	0.1466	0.2566	0.0239	0.0279	-0.0544	-0.1249	0.0356	-0.0735	-0.038	-0.0235	-0	0.2562	-0.0275	-0.0016	0.1909	-0.02	0.1961	2.5802	-32.0884	-28.3348
11	0.0814	0.035	-0.0521	0.4744	0.0541	0.4485	-0.0353	0.0337	-0.0034	-0.1135	0.085	-0.1231	0.0034	0.0494	0	0.1899	-0.014	-0.0069	0.1516	-0.0379	0.1771	6.6912	-42.7719	-28.4113
12	0.2391	0.0685	0.0597	0.2924	0.0621	0.0194	-0.0144	0.0545	-0.0773	0.0336	0.1017	-0.1772	0.2109	0.0477	-0.0002	0.2589	-0.0228	-0.0245	0.207	-0.0339	0.2367	6.5441	-45.5431	-16.544
13	0.1746	0.2112	0.1795	0.5979	0.3343	0.3169	0.0274	-0.0034	-0.0515	0.042	0.0727	-0.1867	0.1136	0.0878	0.0077	0.2207	0.0259	-0.0465	0.1672	-0.032	0.2472	9.9843	-45.8579	-14.9376
14	0.4124	-0.0908	-0.3838	0.1232	-0.1554	1.0909	0.0907	0.0457	-0.308	0.171	0.0645	-0.1174	0.6022	-0.2651	0.0929	0.4135	0.0922	-0.1372	-0.0059	-0.0792	0.351	6.9017	-64.961	-16.2928
15	0.0502	0.0127	-0.0233	0.034	0.0359	0.0478	0.0976	-0.1546	-0.058	0.2876	0.0092	-0.0659	0.2427	-0.0236	-0	0.3677	-0.0269	-0.0827	0.1884	0.0155	0.2332	-1.6476	-51.2583	-0.2338
16	0.0145	-0.0081	-0.0204	0.1004	0.0918	0.104	-0.0713	-0.0316	-0.1227	0.1513	0.0845	-0.1673	0.1011	0.1266	0	0.2486	0.0007	-0.0639	0.2489	-0.0168	0.2618	11.9039	-35.0517	-3.0347

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 176 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 177 through 235 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 236 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 139 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 140 through 207 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 208 through 235 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 236 through 338 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 339 through 379 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 380 through 441 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 442 through 461 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 779 molecules

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