PDB-5ma0: PCE reductive dehalogenase from S. multivorans in complex with 2,...

ID or keywords:

Entry

Database: PDB / ID: 5ma0

Title

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

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: 1.9 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	Nov 2, 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

-
Download

PDBx/mmCIF format	5ma0.cif.gz	373 KB	Display	PDBx/mmCIF format
PDB format	pdb5ma0.ent.gz	302.6 KB	Display	PDB format
PDBx/mmJSON format	5ma0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ma0_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5ma0_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5ma0_validation.xml.gz	39.9 KB	Display
Data in CIF	5ma0_validation.cif.gz	59.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma0 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma0	HTTPS FTP

-
Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8yC 5m8zC 5m90C 5m91C 5m92C 5ma1C 5ma2C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5m8z-d 5m90-d 5m8y-d 5obi-d 5m8w-d 5m2g-d 5obp-d 5m8u-d 5ma2-d 4ur2-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

-
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 software

Unit cell

Length a, b, c (Å)	73.577, 73.577, 184.480
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

-
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

-
Non-polymers , 5 types, 695 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.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-DUB / 2,6-dichlorophenol Mass: 163.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₄Cl₂O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: Oct 22, 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: 1.9→31 Å / Num. obs: 76268 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / B_iso Wilson estimate: 25.15 Å² / CC_1/2: 1 / R_merge(I) obs: 0.0656 / Net I/σ(I): 32.33
Reflection shell	Resolution: 1.9→1.968 Å / Redundancy: 9.4 % / R_merge(I) obs: 0.7996 / Mean I/σ(I) obs: 2.69 / CC_1/2: 0.774 / % possible all: 96

-
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: 1.9→30.992 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.32

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1672	3814	4.99 %	Random selection
R_work	0.1361	-	-	-
obs	0.1376	76268	99.14 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→30.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6777	0	264	681	7722

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7318
X-RAY DIFFRACTION	f_angle_d	0.93	9972
X-RAY DIFFRACTION	f_dihedral_angle_d	14.956	4355
X-RAY DIFFRACTION	f_chiral_restr	0.058	1040
X-RAY DIFFRACTION	f_plane_restr	0.006	1326

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 (%)
1.8996-1.9212	0.2877	226	0.2856	4354	X-RAY DIFFRACTION	90
1.9212-1.9438	0.2617	248	0.2531	4723	X-RAY DIFFRACTION	97
1.9438-1.9675	0.2411	245	0.2106	4715	X-RAY DIFFRACTION	98
1.9675-1.9924	0.2259	253	0.1807	4802	X-RAY DIFFRACTION	99
1.9924-2.0186	0.2412	248	0.1769	4708	X-RAY DIFFRACTION	99
2.0186-2.0462	0.1848	250	0.1537	4772	X-RAY DIFFRACTION	99
2.0462-2.0755	0.189	254	0.1464	4833	X-RAY DIFFRACTION	99
2.0755-2.1064	0.1715	254	0.1444	4808	X-RAY DIFFRACTION	99
2.1064-2.1393	0.1748	250	0.1511	4724	X-RAY DIFFRACTION	99
2.1393-2.1744	0.1813	249	0.143	4781	X-RAY DIFFRACTION	99
2.1744-2.2119	0.1886	254	0.1323	4835	X-RAY DIFFRACTION	99
2.2119-2.2521	0.1674	254	0.1357	4811	X-RAY DIFFRACTION	99
2.2521-2.2954	0.1815	250	0.1288	4791	X-RAY DIFFRACTION	100
2.2954-2.3422	0.1863	251	0.1306	4758	X-RAY DIFFRACTION	100
2.3422-2.3932	0.1702	252	0.1337	4833	X-RAY DIFFRACTION	100
2.3932-2.4488	0.1728	259	0.1293	4905	X-RAY DIFFRACTION	100
2.4488-2.51	0.1539	250	0.1248	4734	X-RAY DIFFRACTION	100
2.51-2.5778	0.1845	257	0.1313	4870	X-RAY DIFFRACTION	100
2.5778-2.6537	0.1683	255	0.1331	4853	X-RAY DIFFRACTION	100
2.6537-2.7393	0.166	255	0.1289	4825	X-RAY DIFFRACTION	100
2.7393-2.8371	0.1788	257	0.1363	4842	X-RAY DIFFRACTION	100
2.8371-2.9506	0.1946	252	0.1364	4798	X-RAY DIFFRACTION	100
2.9506-3.0848	0.1644	253	0.1354	4813	X-RAY DIFFRACTION	100
3.0848-3.2473	0.1764	251	0.1333	4820	X-RAY DIFFRACTION	100
3.2473-3.4505	0.1451	256	0.1232	4851	X-RAY DIFFRACTION	100
3.4505-3.7165	0.1545	252	0.1236	4816	X-RAY DIFFRACTION	100
3.7165-4.0897	0.1432	255	0.1165	4870	X-RAY DIFFRACTION	100
4.0897-4.6798	0.1258	252	0.1124	4801	X-RAY DIFFRACTION	100
4.6798-5.8894	0.1616	257	0.1322	4851	X-RAY DIFFRACTION	100
5.8894-30.9958	0.1463	253	0.1492	4796	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	0.4811	0.1122	0.3833	0.6904	0.372	0.4934	-0.0705	-0.0419	0.1163	-0.131	0.0541	0.0645	-0.2043	-0.1302	-0.0002	0.2471	0.0191	-0.0263	0.1547	-0.0082	0.1983	-8.4676	-12.2172	-11.1819
2	0.1632	-0.0389	0.0574	0.6427	0.3547	0.7988	0.0034	0.0063	0.0109	-0.0686	-0.0059	0.0414	-0.0241	-0.1136	0.0001	0.1702	-0.0182	-0.024	0.1745	-0.0119	0.1777	-10.0492	-29.1056	-13.1256
3	0.2539	-0.2227	0.0161	0.7456	0.2999	0.488	0.0052	-0.0226	0.0181	-0.1277	-0.0375	0.1202	-0.1171	-0.1504	-0.0001	0.1987	-0.0081	-0.0556	0.2296	0.0012	0.2011	-16.3147	-23.1052	-15.9914
4	0.2436	-0.0298	-0.0594	0.6645	0.055	0.5797	0.0067	-0.0493	0.0124	0.0193	-0.0223	0.045	-0.072	-0.0887	-0	0.1635	-0.0015	-0.0279	0.1573	-0.0233	0.1462	-9.87	-23.0632	-3.7691
5	0.095	0.1187	0.1254	0.1396	0.1785	0.1174	0.0503	0.0151	0.1558	-0.0977	-0.0271	0.0166	-0.377	-0.1117	-0.0004	0.3401	0.0367	-0.0309	0.1561	-0.0273	0.2083	-9.6003	-3.8846	-7.0502
6	0.1138	0.038	-0.0283	0.1825	0.0686	0.119	-0.0671	-0.1404	0.031	-0.0044	-0.032	-0.0536	-0.1882	0.396	-0.0002	0.21	-0.0015	-0.0214	0.2238	-0.0099	0.1851	2.2281	-16.1279	5.1692
7	-0.0741	0.1576	0.0297	0.0558	0.1963	0.219	0.0111	-0.2353	0.0098	0.2056	0.0879	-0.1067	0.0396	0.2425	0.0232	0.2266	-0.0654	-0.0306	0.2586	-0.0604	0.2345	4.1554	-25.9313	3.3899
8	0.1379	0.1312	-0.3219	0.5297	-0.2279	0.6185	0.0333	-0.0452	-0.0728	-0.0018	0.0646	-0.2554	0.4151	0.1169	0.0501	0.3111	0.0414	-0.0164	0.2295	-0.0929	0.3233	8.8365	-56.555	-19.8502
9	0.0873	-0.0302	-0.1026	0.1263	0.1668	0.1113	0.0121	-0.0381	-0.0377	0.122	0.0093	0.0409	0.3096	-0.1025	0.0017	0.3314	-0.1015	-0.0367	0.187	0.0153	0.1963	-15.08	-55.2899	-8.5357
10	0.1034	-0.1127	-0.1231	0.3594	0.1063	0.5388	-0.0159	0.0636	-0.0377	-0.149	0.1113	-0.1478	-0.0109	0.0602	0.0001	0.2211	-0.0385	0.0085	0.1848	-0.0535	0.2134	7.2189	-35.6592	-24.8912
11	0.3247	0.0669	-0.0018	0.7645	0.3564	0.4035	0.0097	0.0745	-0.0787	-0.156	0.1147	-0.1661	0.0958	0.0425	0.0016	0.2243	-0.0379	-0.0013	0.1699	-0.0395	0.1738	2.8373	-45.7477	-27.4595
12	0.4558	0.2264	0.1437	0.8367	0.3838	0.9341	0.0344	0.0149	-0.0938	0.0508	0.1144	-0.2307	0.2181	0.1394	0.1304	0.229	0.0424	-0.0553	0.1533	-0.058	0.262	9.1281	-51.5185	-15.3363
13	0.1078	-0.1059	0.1871	0.2595	0.2547	0.4158	0.0517	-0.0744	-0.0224	0.211	0.048	-0.1359	0.1779	0.0782	0.0049	0.2587	-0.006	-0.0766	0.1759	-0.0062	0.206	4.8391	-43.6638	-1.5681

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 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 96 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 97 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 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 695 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 695 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 695 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi