PDB-5m91: PCE reductive dehalogenase from S. multivorans in complex with 2,...

ID or keywords:

Entry

Database: PDB / ID: 5m91

Title

PCE reductive dehalogenase from S. multivorans in complex with 2,6-dibromophenol

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 / metal ion binding / identical protein binding
Similarity search - Function

Biological species

Sulfurospirillum multivorans DSM 12446 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.719 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 31, 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_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5m91.cif.gz	378.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5m91.ent.gz	306.4 KB	Display	PDB format
PDBx/mmJSON format	5m91.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5m91_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5m91_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5m91_validation.xml.gz	42.1 KB	Display
Data in CIF	5m91_validation.cif.gz	62.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/5m91 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m91	HTTPS FTP

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Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8yC 5m8zC 5m90C 5m92C 5ma0C 5ma1C 5ma2C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ma2-d 5m8u-d 5m8w-d 5obp-d 5obi-d 5m2g-d 5m8z-d 5m8x-d 4uqu-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 (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)	73.541, 73.541, 184.613
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, 817 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.: 1 / Source method: obtained synthetically / Formula: C₇H₈N₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-94N / 2,6-bis(bromanyl)phenol Mass: 251.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₄Br₂O
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 801 / 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: Nov 19, 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: 1.719→30.2 Å / Num. obs: 103500 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / B_iso Wilson estimate: 20.72 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.0673 / Net I/σ(I): 22.07
Reflection shell	Resolution: 1.719→1.781 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.7619 / Mean I/σ(I) obs: 2.59 / CC_1/2: 0.799 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS	January 10, 2014	data reduction
XDS	January 10, 2014	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UQU

4uqu

Resolution: 1.719→30.106 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 17.51

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1746	5175	5 %	Random selection
R_work	0.1463	-	-	-
obs	0.1477	103500	99.69 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 28.45 Å²

Refinement step

Cycle: LAST / Resolution: 1.719→30.106 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6795	0	279	801	7875

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7361
X-RAY DIFFRACTION	f_angle_d	0.964	10026
X-RAY DIFFRACTION	f_dihedral_angle_d	15.31	4391
X-RAY DIFFRACTION	f_chiral_restr	0.059	1043
X-RAY DIFFRACTION	f_plane_restr	0.006	1350

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 (%)
1.7191-1.7387	0.2708	333	0.2686	6334	X-RAY DIFFRACTION	98
1.7387-1.7591	0.2728	341	0.2455	6530	X-RAY DIFFRACTION	100
1.7591-1.7806	0.3149	340	0.2477	6472	X-RAY DIFFRACTION	100
1.7806-1.8031	0.2866	345	0.2366	6559	X-RAY DIFFRACTION	100
1.8031-1.8268	0.2444	345	0.2265	6553	X-RAY DIFFRACTION	100
1.8268-1.8518	0.2769	337	0.2202	6422	X-RAY DIFFRACTION	100
1.8518-1.8783	0.2209	345	0.21	6568	X-RAY DIFFRACTION	100
1.8783-1.9063	0.209	341	0.1901	6467	X-RAY DIFFRACTION	100
1.9063-1.9361	0.2072	346	0.189	6546	X-RAY DIFFRACTION	100
1.9361-1.9678	0.2187	341	0.1778	6486	X-RAY DIFFRACTION	100
1.9678-2.0018	0.2061	344	0.1746	6501	X-RAY DIFFRACTION	100
2.0018-2.0382	0.2238	342	0.1712	6518	X-RAY DIFFRACTION	100
2.0382-2.0773	0.1864	343	0.1613	6508	X-RAY DIFFRACTION	100
2.0773-2.1197	0.2036	337	0.1611	6440	X-RAY DIFFRACTION	100
2.1197-2.1658	0.1749	346	0.1509	6539	X-RAY DIFFRACTION	100
2.1658-2.2162	0.1901	343	0.1476	6461	X-RAY DIFFRACTION	100
2.2162-2.2716	0.1611	337	0.1403	6408	X-RAY DIFFRACTION	100
2.2716-2.333	0.1764	343	0.1346	6515	X-RAY DIFFRACTION	100
2.333-2.4016	0.1736	342	0.1381	6487	X-RAY DIFFRACTION	100
2.4016-2.4791	0.1509	345	0.1364	6519	X-RAY DIFFRACTION	100
2.4791-2.5677	0.1868	346	0.1407	6511	X-RAY DIFFRACTION	100
2.5677-2.6704	0.1771	340	0.1361	6490	X-RAY DIFFRACTION	100
2.6704-2.7918	0.1568	342	0.1339	6485	X-RAY DIFFRACTION	100
2.7918-2.9389	0.1759	345	0.1372	6560	X-RAY DIFFRACTION	100
2.9389-3.1229	0.1715	337	0.1379	6449	X-RAY DIFFRACTION	100
3.1229-3.3637	0.1806	347	0.1353	6533	X-RAY DIFFRACTION	100
3.3637-3.7017	0.1589	345	0.1261	6497	X-RAY DIFFRACTION	100
3.7017-4.236	0.1291	342	0.1135	6490	X-RAY DIFFRACTION	100
4.236-5.3321	0.1437	346	0.1177	6492	X-RAY DIFFRACTION	100
5.3321-30.1102	0.142	338	0.142	6508	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	0.1036	0.1353	0.0716	0.1835	0.2079	0.1251	0.0936	-0.1138	-0.0106	0.0106	-0.0055	0.1344	0.0071	-0.1986	0	0.191	0.0379	-0.0201	0.2478	-0.0289	0.2009	-14.9106	-18.0729	4.7198
2	0.0643	0.1269	0.1138	0.544	0.4442	0.7321	-0.0245	0.0316	-0.0156	-0.1587	-0.0005	0.0156	-0.111	-0.114	-0.0001	0.1848	-0.0063	-0.0231	0.1402	0.0021	0.159	-7.8825	-23.7289	-16.0462
3	0.0599	-0.0483	0.02	0.2386	0.0639	0.0435	0.0261	0.0583	0.0479	-0.4778	-0.1285	0.1605	-0.2048	-0.2954	-0.0128	0.2596	0.0418	-0.133	0.3371	-0.0652	0.2471	-23.0537	-23.1517	-23.8409
4	0.0142	0.025	-0.0444	0.4579	0.0861	0.6061	0.0225	-0.0426	-0.0047	-0.0153	-0.0348	0.0069	-0.0899	-0.1238	-0.0015	0.1435	-0.0021	-0.0256	0.1477	-0.0231	0.1426	-9.6266	-22.9375	-4.4195
5	0.0407	0.0577	0.0622	0.0833	0.1124	0.066	0.0001	-0.0234	0.1318	-0.1189	-0.0163	0.0251	-0.3945	-0.1251	-0.0001	0.3568	0.0567	-0.0304	0.1594	-0.0248	0.1974	-9.5847	-3.9813	-7.0854
6	0.1212	-0.0124	0.0051	0.0698	0.0387	0.0524	-0.0631	-0.1398	0.0343	-0.0519	-0.017	-0.0303	-0.1206	0.2074	0.002	0.2156	-0.0084	-0.0127	0.1894	-0.0068	0.1703	2.2257	-16.2475	5.1832
7	-0.0378	0.1225	-0.0246	0.0063	0.1482	0.1122	0.0462	-0.2778	-0.0199	0.1639	0.037	-0.0967	0.0114	0.219	0.0271	0.1919	-0.0723	-0.026	0.2163	-0.0554	0.2007	4.1323	-26.0531	3.4117
8	0.0183	-0.0145	-0.1088	0.2242	-0.0151	0.5017	0.0736	-0.0269	0.0306	0.0455	0.0656	-0.2395	0.6215	0.1367	0.0917	0.3124	0.0552	-0.0499	0.191	-0.1123	0.3313	8.7459	-56.7006	-19.806
9	0.1358	-0.0591	-0.088	0.0396	0.0773	0.042	0.0417	0.0157	0.0218	0.1361	0.005	0.034	0.3081	-0.2245	0.0075	0.3449	-0.1443	-0.053	0.1623	0.0052	0.1653	-14.8881	-54.7043	-8.9357
10	0.0122	-0.0068	-0.0441	0.1571	0.2584	0.4921	-0.0085	0.0875	-0.0369	-0.1699	0.107	-0.1267	-0.0329	0.0456	0.0068	0.2065	-0.0311	0.0106	0.1533	-0.0491	0.2051	7.5353	-35.7751	-24.9925
11	0.0407	0.0537	0.016	0.0617	0.0449	0.1249	0.0484	0.1178	0.0328	-0.2302	0.083	-0.0099	0.0137	-0.0817	0.0032	0.3021	-0.0571	0.0046	0.1815	-0.0431	0.1692	-0.4676	-46.16	-36.443
12	0.1767	0.0555	0.0917	0.1979	-0.0012	0.0872	-0.0308	0.0042	-0.1105	-0.032	0.144	-0.2357	0.4053	0.0936	0.087	0.2443	-0.0403	-0.0115	0.1635	-0.0497	0.2204	6.6285	-45.6524	-16.498
13	0.2653	0.2982	0.1728	0.5462	0.5089	0.7554	0.0823	0.0583	-0.082	0.0858	0.1184	-0.2057	0.2585	0.1075	0.282	0.2386	0.0422	-0.0764	0.0999	-0.0599	0.2498	9.0309	-51.663	-15.2894
14	0.0342	0.0376	-0.0095	0.0337	-0.0156	0.1386	0.1575	-0.1485	-0.0623	0.3024	-0.0189	-0.0696	0.3831	-0.1244	0.0646	0.3848	-0.0458	-0.0977	0.1445	0.0126	0.207	-1.4672	-51.3328	-0.2
15	0.0076	-0.0152	-0.0088	0.0449	0.0422	0.0494	-0.0148	0.0095	-0.0871	0.1329	0.0994	-0.1158	0.1423	0.1553	0.0001	0.1832	0.0038	-0.06	0.2145	-0.0333	0.2187	12.0029	-35.168	-3.0551

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 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 207 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 208 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 207 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 208 through 235 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 236 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, 817 molecules

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