PDB-5m92: PCE reductive dehalogenase from S. multivorans in complex with 2,...

ID or keywords:

Entry

Database: PDB / ID: 5m92

Title

PCE reductive dehalogenase from S. multivorans in complex with 2,4-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 / identical protein binding / metal ion binding
Similarity search - Function

Biological species

Sulfurospirillum multivorans DSM 12446 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.785 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 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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PDBx/mmCIF format	5m92.cif.gz	377.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5m92_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	5m92_full_validation.pdf.gz	2.5 MB	Display
Data in XML	5m92_validation.xml.gz	41.4 KB	Display
Data in CIF	5m92_validation.cif.gz	61.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/5m92 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m92	HTTPS FTP

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Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8yC 5m8zC 5m90C 5m91C 5ma0C 5ma1C 5ma2C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5maa-d 4ur1-d 4ur3-1 4ur2-d 5m8y-d 4ur3-2 4ur3-3 2bpo-2 5m8z-d 1one-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 (15) #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) #122 - Feb 2010 Enhanceosome similarity (1) #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 (15)
#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)
#122 - Feb 2010
Enhanceosome
similarity (1)
#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)	73.944, 73.944, 185.109
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 , 7 types, 752 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.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-Y8I / 2,4-bis(bromanyl)phenol Mass: 251.903 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₄Br₂O
#7: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 731 / 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: Feb 3, 2015
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: 1.785→47.4 Å / Num. obs: 93436 / % possible obs: 99.49 % / Observed criterion σ(I): 2 / Redundancy: 13.56 % / B_iso Wilson estimate: 24.06 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / Net I/σ(I): 22
Reflection shell	Resolution: 1.785→1.849 Å / Redundancy: 13.41 % / R_merge(I) obs: 0.951 / Mean I/σ(I) obs: 2.4 / CC_1/2: 0.752 / % possible all: 94.94

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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: 1.785→47.375 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.92

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.178	1059	1.13 %	Random selection
R_work	0.149	-	-	-
obs	0.1493	93432	99.42 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.785→47.375 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6795	0	316	731	7842

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7398
X-RAY DIFFRACTION	f_angle_d	0.928	10074
X-RAY DIFFRACTION	f_dihedral_angle_d	14.821	4385
X-RAY DIFFRACTION	f_chiral_restr	0.059	1043
X-RAY DIFFRACTION	f_plane_restr	0.006	1340

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 (%)
1.7846-1.8261	0.3284	128	0.2796	11231	X-RAY DIFFRACTION	91
1.8261-1.8718	0.3119	141	0.2515	12227	X-RAY DIFFRACTION	100
1.8718-1.9224	0.2497	142	0.2289	12325	X-RAY DIFFRACTION	100
1.9224-1.979	0.2507	139	0.2018	12302	X-RAY DIFFRACTION	100
1.979-2.0428	0.2339	142	0.186	12316	X-RAY DIFFRACTION	100
2.0428-2.1158	0.1997	142	0.1716	12303	X-RAY DIFFRACTION	100
2.1158-2.2006	0.1998	139	0.168	12247	X-RAY DIFFRACTION	100
2.2006-2.3007	0.1928	141	0.1581	12339	X-RAY DIFFRACTION	100
2.3007-2.422	0.2538	140	0.1543	12231	X-RAY DIFFRACTION	100
2.422-2.5737	0.1738	140	0.1498	12255	X-RAY DIFFRACTION	100
2.5737-2.7724	0.1528	143	0.1432	12367	X-RAY DIFFRACTION	100
2.7724-3.0514	0.1678	142	0.1401	12286	X-RAY DIFFRACTION	100
3.0514-3.4928	0.1625	142	0.1311	12316	X-RAY DIFFRACTION	100
3.4928-4.4001	0.1363	141	0.1147	12270	X-RAY DIFFRACTION	100
4.4001-47.3921	0.1436	140	0.1321	12285	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	0.3297	0.2974	-0.0194	0.3292	0.457	0.4096	0.037	-0.1388	0.0524	0.0684	-0.0551	0.1556	-0.0477	-0.2748	0.0002	0.2323	0.0132	-0.0003	0.258	-0.0657	0.2197	-15.3733	-17.6698	4.4419
2	0.2395	0.0358	0.0483	0.717	0.2939	0.439	-0.0103	0.0228	0.0419	-0.1196	-0.0316	0.0389	-0.1026	-0.0448	-0.0005	0.2097	-0.0229	-0.0386	0.1535	-0.012	0.1586	-7.8328	-23.3466	-16.2246
3	0.2351	0.0906	-0.0534	1.029	0.243	0.7273	-0.0213	0.0402	0.0639	-0.1214	-0.055	0.1745	-0.1389	-0.1688	0	0.1841	0.0063	-0.0599	0.2065	-0.0281	0.1949	-17.0247	-22.9172	-16.4685
4	0.1795	0.1614	0.004	0.7755	0.1811	0.6795	0.0234	-0.0513	0.0313	0.0487	-0.0653	0.0685	-0.0292	-0.0845	0	0.1803	-0.012	-0.036	0.1622	-0.0326	0.1502	-10.2039	-22.5408	-3.7131
5	0.1244	0.1822	0.2053	0.1938	0.217	0.2435	-0.0184	0.0205	0.1699	-0.0694	-0.052	0.0322	-0.3505	-0.0697	0	0.3182	0.022	-0.0526	0.1491	-0.0363	0.2114	-9.8776	-3.48	-7.1379
6	0.1716	0.1216	0.0464	0.1561	0.1427	0.0859	-0.094	-0.1171	-0.0133	-0.0272	-0.0662	-0.0163	-0.1159	0.1614	-0.0001	0.2189	-0.0178	-0.0237	0.1982	-0.0022	0.1933	1.892	-16.0545	5.1718
7	-0.2726	0.2612	-0.1176	0.0773	0.385	0.3613	-0.0277	-0.121	-0.0082	0.1791	0.1139	-0.0622	0.1251	0.1258	0.0217	0.1918	-0.0537	-0.0516	0.214	-0.0345	0.2151	3.7889	-25.6959	3.4743
8	-0.0343	0.1849	-0.1511	0.79	-0.0877	0.6565	0.0187	0.1183	-0.0888	0.0744	0.1162	-0.2565	0.3414	0.1549	0.0178	0.2667	0.0378	-0.04	0.202	-0.091	0.3093	8.6978	-56.4463	-19.7554
9	0.2417	-0.1078	-0.1026	0.2028	0.3029	0.2401	0.0608	-0.0226	-0.039	0.15	-0.0502	0.0417	0.1789	-0.1069	0.0227	0.2754	-0.0847	-0.031	0.1365	0.0019	0.1751	-15.1296	-54.4605	-9.0531
10	0.2181	0.0097	0.1086	0.4984	0.3131	0.6974	-0.0211	0.0784	-0.0284	-0.1428	0.1079	-0.1998	-0.0875	0.0777	0.0001	0.2139	-0.0443	0.0035	0.1982	-0.0355	0.2188	7.539	-35.4125	-25.0049
11	0.3606	0.1128	-0.0108	0.963	0.4877	0.3486	0.0083	0.099	-0.0816	-0.127	0.0846	-0.1462	0.0556	0.0722	0.0008	0.2213	-0.0392	-0.004	0.1975	-0.0248	0.1974	2.7626	-45.6249	-27.4324
12	0.1904	0.2019	0.1546	0.8719	0.2282	0.6817	0.0571	0.0358	-0.1007	0.0873	0.0691	-0.2331	0.165	0.1332	0.0167	0.2194	0.0276	-0.0742	0.1484	-0.046	0.2586	8.922	-51.3887	-15.1859
13	0.0423	0.0067	0.1386	0.1788	0.2047	0.4406	0.0916	-0.0584	-0.0591	0.2663	0.0005	-0.1418	0.1362	0.0411	0.0009	0.2822	-0.0129	-0.095	0.1828	0.0099	0.2433	4.4826	-43.5227	-1.4264

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 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 379 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 380 through 461 )

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