PDB-5obp: PCE reductive dehalogenase from S. multivorans with 6-hydroxybenz...

ID or keywords:

Entry

Database: PDB / ID: 5obp

Title

PCE reductive dehalogenase from S. multivorans with 6-hydroxybenzimidazolyl norcobamide cofactor

Components

Tetrachloroethene reductive dehalogenase catalytically active subunit

Keywords

OXIDOREDUCTASE / organohalide respiration / anaerobic crystallisation /

cobalamin

Function / homology

Function and homology information

tetrachloroethene reductive dehalogenase / 4 iron, 4 sulfur cluster binding /

oxidoreductase activity /

metal ion binding /

plasma membrane /

cytoplasm
Similarity search - Function

Biological species

Sulfurospirillum multivorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.593 Å

Authors

Keller, S. / Kunze, C. / Bommer, M. / Paetz, C. / Menezes, R.C. / Svatos, A. / Dobbek, H. / Schubert, T.

Funding support

Germany, 2items

Citation

Journal: J. Bacteriol. / Year: 2018
Title: Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans.
Authors: Keller, S. / Kunze, C. / Bommer, M. / Paetz, C. / Menezes, R.C. / Svatos, A. / Dobbek, H. / Schubert, T.

History

Deposition	Jun 28, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2018	Group: Database references / Category: citation / Item: _citation.title
Revision 1.2	Mar 28, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3	Apr 4, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4	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	5obp.cif.gz	377 KB	Display	PDBx/mmCIF format
PDB format	pdb5obp.ent.gz	304.4 KB	Display	PDB format
PDBx/mmJSON format	5obp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/5obp ftp://data.pdbj.org/pub/pdb/validation_reports/ob/5obp	HTTPS FTP

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Related structure data

Related structure data	5obiC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ma2-d 5m8u-d 5m2g-d 5obi-d 5m91-d 5m90-d 5m8z-d 5m8w-d 5ma0-d 5m8x-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 catalytically active subunit

B: Tetrachloroethene reductive dehalogenase catalytically active subunit

hetero molecules

109 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.565, 73.565, 184.677
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 catalytically active subunit Mass: 52164.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfurospirillum multivorans (bacteria) / References: UniProt: O68252

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Non-polymers , 5 types, 875 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-9QQ / 6-hydroxybenzimidazolyl-norcobamide Mass: 1304.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅₉H₈₃CoN₁₃O₁₅P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-BEN / BENZAMIDINE / 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 / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 864 / 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: PETRA III, DESY / Beamline: P11 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2016
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: 1.593→36.074 Å / Num. obs: 129361 / % possible obs: 99.33 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / B_iso Wilson estimate: 18.95 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.1139 / R_pim(I) all: 0.0325 / Net I/σ(I): 14.92
Reflection shell	Resolution: 1.593→1.65 Å / Redundancy: 12.6 % / R_merge(I) obs: 0.9312 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 12146 / CC_1/2: 0.802 / R_pim(I) all: 0.2697 / % possible all: 93.44

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575)	refinement
XDS	Nov 1, 2016	data reduction
XDS	Nov 1, 2016	data scaling
PHENIX	(1.11.1_2575)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UQU

4uqu

Resolution: 1.593→36.074 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 16.8

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1766	6455	5 %	Random Selection
R_work	0.1524	-	-	-
obs	0.1536	129111	99.25 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.593→36.074 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6796	0	243	864	7903

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7310
X-RAY DIFFRACTION	f_angle_d	0.93	9961
X-RAY DIFFRACTION	f_dihedral_angle_d	3.881	6005
X-RAY DIFFRACTION	f_chiral_restr	0.059	1055
X-RAY DIFFRACTION	f_plane_restr	0.006	1327

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 (%)
1.5932-1.6113	0.3439	330	0.3134	6295	X-RAY DIFFRACTION	78
1.6113-1.6303	0.2797	438	0.2433	8329	X-RAY DIFFRACTION	100
1.6303-1.6502	0.252	429	0.2348	8146	X-RAY DIFFRACTION	100
1.6502-1.6711	0.2639	428	0.2356	8202	X-RAY DIFFRACTION	100
1.6711-1.693	0.2637	428	0.2261	8114	X-RAY DIFFRACTION	100
1.693-1.7162	0.2386	435	0.2173	8262	X-RAY DIFFRACTION	100
1.7162-1.7408	0.2145	428	0.2024	8139	X-RAY DIFFRACTION	100
1.7408-1.7667	0.214	437	0.1925	8264	X-RAY DIFFRACTION	100
1.7667-1.7943	0.1986	435	0.198	8231	X-RAY DIFFRACTION	100
1.7943-1.8238	0.2131	426	0.1918	8112	X-RAY DIFFRACTION	100
1.8238-1.8552	0.1894	432	0.1821	8202	X-RAY DIFFRACTION	100
1.8552-1.8889	0.2007	439	0.1771	8343	X-RAY DIFFRACTION	100
1.8889-1.9253	0.1909	425	0.1684	8060	X-RAY DIFFRACTION	100
1.9253-1.9646	0.1836	432	0.1612	8182	X-RAY DIFFRACTION	100
1.9646-2.0073	0.1905	429	0.1605	8228	X-RAY DIFFRACTION	100
2.0073-2.054	0.1883	428	0.1574	8131	X-RAY DIFFRACTION	100
2.054-2.1053	0.1914	436	0.1575	8267	X-RAY DIFFRACTION	100
2.1053-2.1622	0.1697	435	0.1532	8219	X-RAY DIFFRACTION	100
2.1622-2.2259	0.1656	430	0.1447	8148	X-RAY DIFFRACTION	100
2.2259-2.2977	0.1796	432	0.1486	8206	X-RAY DIFFRACTION	100
2.2977-2.3798	0.1907	431	0.1506	8187	X-RAY DIFFRACTION	100
2.3798-2.4751	0.1843	427	0.1511	8184	X-RAY DIFFRACTION	100
2.4751-2.5877	0.1717	432	0.1484	8158	X-RAY DIFFRACTION	100
2.5877-2.7241	0.1903	434	0.1454	8246	X-RAY DIFFRACTION	100
2.7241-2.8947	0.1647	429	0.1444	8134	X-RAY DIFFRACTION	100
2.8947-3.118	0.1639	430	0.1435	8230	X-RAY DIFFRACTION	100
3.118-3.4316	0.1558	429	0.1363	8190	X-RAY DIFFRACTION	100
3.4316-3.9276	0.1409	433	0.1257	8199	X-RAY DIFFRACTION	100
3.9276-4.9464	0.1481	433	0.1205	8196	X-RAY DIFFRACTION	100
4.9464-36.0832	0.162	430	0.1437	8180	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	0.1222	0.1356	0.0197	0.2511	0.2186	0.1913	0.0321	-0.1579	0.0569	0.0454	-0.033	0.1217	-0.0461	-0.1909	0.0001	0.1875	0.0235	-0.0186	0.2355	-0.0483	0.1916	-13.6565	-18.4246	5.3896
2	0.2073	-0.1481	0.0832	0.3835	0.3207	0.4483	-0.0444	0.0798	0.0305	-0.2835	0.0509	-0.0314	-0.2348	-0.0096	0.0025	0.2914	-0.0285	-0.0126	0.1285	0.0009	0.1556	-0.8173	-16.235	-21.9884
3	0.0585	-0.0431	0.0279	0.1368	0.0105	0.0111	-0.0014	-0.0338	0.0047	0.0597	-0.0701	0.097	0.1285	-0.1308	-0	0.1962	-0.0632	-0.0003	0.1965	-0.0273	0.1692	-17.7409	-43.4747	-6.7735
4	0.2864	0.1303	-0.0428	0.6806	0.1869	0.6844	0.0071	-0.04	0.0408	-0.0665	-0.0519	0.0731	-0.1269	-0.1133	-0.0003	0.1666	0.0192	-0.034	0.1473	-0.0317	0.1529	-11.8436	-19.2429	-8.0991
5	-0.0103	-0.0098	-0.0238	0.043	0.0395	0.0276	0.0089	-0.1336	0.0673	0.0232	0.0179	-0.0011	-0.2492	0.3531	0.0001	0.2208	-0.0308	-0.016	0.2712	-0.0374	0.1722	3.341	-17.1351	12.1973
6	0.0155	0.0387	0.0399	0.096	0.0965	0.0917	0.0465	-0.1802	0.1078	0.0904	0.0186	-0.0148	0.0227	0.1104	0.0017	0.1908	-0.0446	-0.0201	0.1915	-0.0352	0.202	4.1538	-30.6682	0.3836
7	0.036	0.0483	-0.0249	0.1303	-0.165	0.1692	0.0982	-0.0744	-0.0601	-0.0915	0.0494	-0.3321	0.1061	0.1215	0.015	0.1704	0.0424	-0.0111	0.2346	-0.1204	0.366	20.018	-52.8914	-18.4538
8	0.1594	0.0634	-0.0474	0.1303	0.1277	0.1636	0.0194	0.0138	-0.0288	0.1076	-0.0182	0.0054	0.2315	-0.1592	0.0149	0.2795	-0.0833	-0.0206	0.1596	-0.0061	0.1692	-13.1699	-57.2209	-12.5689
9	0.0619	-0.0788	-0.0092	0.2644	0.3182	0.4219	-0.0175	0.0456	-0.0292	-0.1581	0.0827	-0.1203	-0.0623	0.0535	0.0092	0.2018	-0.0291	0.0091	0.1543	-0.035	0.1792	7.7811	-35.9172	-25.0096
10	0.0711	-0.0214	0.0131	0.32	0.0792	0.1588	-0.0666	0.0705	-0.0462	-0.2065	0.0985	-0.0832	-0.0233	-0.0248	0.0005	0.2722	-0.0576	0.0198	0.2016	-0.0421	0.1747	4.0429	-44.6057	-33.5536
11	0.0666	0.0618	0.0246	0.2124	0.2249	0.1829	0.0483	-0.0219	-0.0509	0.0521	-0.021	-0.0651	0.0635	0.0491	0.0027	0.1771	-0.0217	-0.0261	0.119	-0.0137	0.1438	0.6166	-42.5521	-11.8518
12	0.1468	0.1501	0.0752	0.2506	0.2414	0.2304	0.0313	0.0288	-0.1082	-0.0007	0.0915	-0.2313	0.0901	0.146	0.02	0.2068	0.0241	-0.0418	0.1613	-0.0398	0.263	13.8863	-49.1026	-14.2484
13	0.1407	0.0295	-0.0999	0.0023	0.0241	0.4298	0.0519	0.0573	-0.3096	0.0694	0.0571	-0.1455	0.4	-0.0733	0.0338	0.3295	0.0408	-0.0596	0.1193	-0.0474	0.3213	6.6207	-65.2075	-16.1776
14	0.0567	0.0416	0.1202	0.1158	0.1863	0.3026	0.1058	-0.1179	-0.0601	0.1723	-0.03	-0.1107	0.1519	0.0623	-0.0001	0.2305	-0.0185	-0.0439	0.1717	-0.0014	0.1968	4.9319	-43.9266	-1.493

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 119 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 120 through 153 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 389 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 390 through 431 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 432 through 462 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 8 through 35 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 36 through 98 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 99 through 176 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 177 through 224 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 225 through 262 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 263 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 461 )

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