PDB-5ma2: PCE reductive dehalogenase from S. multivorans in complex with 4-...

ID or keywords:

Entry

Database: PDB / ID: 5ma2

Title

PCE reductive dehalogenase from S. multivorans in complex with 4-iodophenol

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: 1.879 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 3, 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.ptnr2_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ma2.cif.gz	379 KB	Display	PDBx/mmCIF format
PDB format	pdb5ma2.ent.gz	306.9 KB	Display	PDB format
PDBx/mmJSON format	5ma2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ma2_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5ma2_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5ma2_validation.xml.gz	42.1 KB	Display
Data in CIF	5ma2_validation.cif.gz	62.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma2 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma2	HTTPS FTP

-
Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8yC 5m8zC 5m90C 5m91C 5m92C 5ma0C 5ma1C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5m91-d 5m8u-d 5obp-d 5m2g-d 5obi-d 5m8x-d 4uqu-d 5m8w-d 5m8z-d 5m90-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 (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

111 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)	73.765, 73.765, 184.711
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 catalytically active subunit Mass: 52164.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfurospirillum multivorans (bacteria) / Plasmid details: DSM-12446 / References: UniProt: O68252

-
Non-polymers , 7 types, 743 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.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-IOL / 4-IODOPHENOL Mass: 220.008 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₅IO
#7: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 720 / 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: 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: 1.879→47.3 Å / Num. obs: 79051 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 11 % / B_iso Wilson estimate: 26.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.082 / Net I/σ(I): 19.29
Reflection shell	Resolution: 1.879→1.946 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7142 / CC_1/2: 0.83 / % possible all: 89

-
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: 1.879→47.268 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 15.51

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1656	3952	5 %	Random selection
R_work	0.1357	-	-	-
obs	0.1372	79047	98.43 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.879→47.268 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6808	0	314	721	7843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7403
X-RAY DIFFRACTION	f_angle_d	0.963	10078
X-RAY DIFFRACTION	f_dihedral_angle_d	16.745	4424
X-RAY DIFFRACTION	f_chiral_restr	0.059	1044
X-RAY DIFFRACTION	f_plane_restr	0.006	1395

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 (%)
1.8791-1.9005	0.2641	205	0.2374	3816	X-RAY DIFFRACTION	75
1.9005-1.9228	0.2487	229	0.2224	4384	X-RAY DIFFRACTION	88
1.9228-1.9463	0.2446	249	0.2074	4745	X-RAY DIFFRACTION	93
1.9463-1.9709	0.2054	261	0.1933	4875	X-RAY DIFFRACTION	98
1.9709-1.9968	0.1944	266	0.1738	5027	X-RAY DIFFRACTION	99
1.9968-2.0242	0.2136	260	0.1662	4974	X-RAY DIFFRACTION	100
2.0242-2.0531	0.2154	269	0.1612	5067	X-RAY DIFFRACTION	100
2.0531-2.0838	0.1966	260	0.1544	4962	X-RAY DIFFRACTION	100
2.0838-2.1163	0.1975	270	0.1587	5112	X-RAY DIFFRACTION	100
2.1163-2.151	0.1958	257	0.1553	4919	X-RAY DIFFRACTION	100
2.151-2.1881	0.1822	265	0.1422	5085	X-RAY DIFFRACTION	100
2.1881-2.2279	0.1866	264	0.1424	5018	X-RAY DIFFRACTION	100
2.2279-2.2707	0.184	264	0.1377	5012	X-RAY DIFFRACTION	100
2.2707-2.3171	0.1571	264	0.1328	5024	X-RAY DIFFRACTION	100
2.3171-2.3675	0.1758	263	0.1368	5043	X-RAY DIFFRACTION	100
2.3675-2.4225	0.1731	267	0.1361	5027	X-RAY DIFFRACTION	100
2.4225-2.4831	0.1914	263	0.1419	4988	X-RAY DIFFRACTION	100
2.4831-2.5503	0.1762	264	0.1399	5072	X-RAY DIFFRACTION	100
2.5503-2.6253	0.1945	262	0.1393	4979	X-RAY DIFFRACTION	100
2.6253-2.71	0.1736	265	0.1313	5006	X-RAY DIFFRACTION	100
2.71-2.8069	0.1564	266	0.1294	5060	X-RAY DIFFRACTION	100
2.8069-2.9192	0.175	262	0.1278	4990	X-RAY DIFFRACTION	100
2.9192-3.0521	0.1498	267	0.1337	5058	X-RAY DIFFRACTION	100
3.0521-3.213	0.1521	267	0.1276	5016	X-RAY DIFFRACTION	100
3.213-3.4142	0.1448	262	0.129	4998	X-RAY DIFFRACTION	100
3.4142-3.6777	0.1477	266	0.1242	5056	X-RAY DIFFRACTION	100
3.6777-4.0476	0.1797	264	0.1161	5002	X-RAY DIFFRACTION	100
4.0476-4.6329	0.1191	262	0.1121	5014	X-RAY DIFFRACTION	100
4.6329-5.8353	0.1552	264	0.1282	5030	X-RAY DIFFRACTION	100
5.8353-47.2832	0.1414	265	0.1419	5007	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	0.8585	0.4322	0.5357	1.2254	0.0344	3.1579	0.0925	-0.231	0.0652	0.1409	-0.0433	0.1074	0.023	-0.2375	-0.0565	0.1769	0.0007	0.0019	0.2135	-0.0539	0.2097	-13.7593	-18.5244	5.488
2	0.5414	0.1511	0.0529	1.004	0.1742	0.9643	-0.0157	-0.0118	0.0672	-0.0612	-0.0023	0.0678	-0.1252	-0.0985	0.0129	0.2265	0.0061	-0.0405	0.1924	-0.0169	0.2028	-10.198	-21.0614	-11.3029
3	0.4026	0.4108	-1.2326	0.4029	-1.0939	3.9328	0.0203	-0.2724	0.0714	0.036	-0.1269	0.0104	-0.174	0.8309	0.1515	0.2716	-0.0113	-0.023	0.3133	-0.0202	0.2313	2.9441	-15.5162	7.4942
4	4.3443	2.5345	-2.0604	2.0646	-1.3213	2.6054	0.3007	-0.4686	0.1915	0.349	-0.1471	-0.0372	-0.1464	0.3647	-0.1794	0.259	-0.0214	-0.0493	0.201	-0.049	0.2578	3.9658	-30.5926	0.3489
5	2.4644	0.4633	-0.207	1.3192	0.0184	1.472	-0.0223	0.0579	-0.0712	-0.002	0.1069	-0.3761	0.3649	0.1915	-0.0585	0.3995	0.0673	-0.0296	0.2019	-0.0622	0.3486	8.5675	-56.8573	-20.1428
6	0.9339	-0.0299	-0.2852	1.0833	0.7924	1.2747	-0.0049	-0.1341	-0.1115	0.2205	-0.0703	0.1585	0.4497	-0.1859	0.0763	0.3875	-0.0934	-0.0399	0.2356	0.0189	0.2511	-14.8813	-54.7859	-8.8911
7	0.5307	-0.0222	0.0044	1.0499	0.277	0.8718	-0.0136	0.1028	-0.025	-0.1861	0.106	-0.1833	-0.0258	0.0936	-0.0883	0.2751	-0.0288	0.0084	0.2276	-0.0347	0.2359	6.5869	-36.1979	-25.6612
8	1.4197	0.5185	-0.5119	1.0488	0.0029	1.7051	-0.036	0.1752	-0.0755	-0.1557	0.1236	-0.1856	0.1102	0.0839	-0.0853	0.3003	-0.0179	-0.0037	0.1751	-0.0435	0.2554	3.6974	-45.8755	-26.4769
9	0.7257	0.2995	0.0877	1.1105	0.2536	0.8996	0.0455	-0.0223	-0.1864	0.0817	0.0713	-0.2771	0.3033	0.1653	-0.0996	0.2905	0.0433	-0.0709	0.178	-0.0463	0.2821	9.0193	-51.6751	-15.3229
10	0.3159	-0.1136	0.1239	0.9263	0.1863	0.9013	0.0534	-0.0911	-0.0832	0.2818	0.0468	-0.1713	0.2402	0.1345	-0.0794	0.3463	-0.0038	-0.084	0.2387	-0.0022	0.2626	4.8907	-43.8981	-1.4548

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 379 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 380 through 431 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 432 through 462 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 52 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 53 through 98 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 99 through 181 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 182 through 235 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 236 through 379 )
10	X-RAY DIFFRACTION	10	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 , 7 types, 743 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 , 7 types, 743 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 , 7 types, 743 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