PDB-5ma1: PCE reductive dehalogenase from S. multivorans in complex with 2,...

ID or keywords:

Entry

Database: PDB / ID: 5ma1

Title

PCE reductive dehalogenase from S. multivorans in complex with 2,4,6-trichlorophenol

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: 2.498 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ma1.cif.gz	350.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ma1.ent.gz	285 KB	Display	PDB format
PDBx/mmJSON format	5ma1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ma1_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5ma1_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5ma1_validation.xml.gz	35 KB	Display
Data in CIF	5ma1_validation.cif.gz	48.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma1 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma1	HTTPS FTP

-
Related structure data

Related structure data	5m2gC 5m8uC 5m8wC 5m8xC 5m8yC 5m8zC 5m90C 5m91C 5m92C 5ma0C 5ma2C 5maaC 4uquS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5m2g-d 5m8x-d 5m8z-d 5m8y-d 5m90-d 4ur2-d 5maa-d 5m8w-d 5m8u-d 5ma2-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)	73.461, 73.461, 179.365
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, 224 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.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-T6C / 2,4,6-trichlorophenol Mass: 197.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₃Cl₃O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 214 / 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: Sep 25, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.9 Å / Relative weight: 1
Reflection	Resolution: 2.498→46.4 Å / Num. obs: 32816 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15 % / B_iso Wilson estimate: 41.92 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.204 / Net I/σ(I): 17.9
Reflection shell	Resolution: 2.498→2.588 Å / Redundancy: 14.1 % / R_merge(I) obs: 1.84 / Mean I/σ(I) obs: 1.59 / CC_1/2: 0.551 / % possible all: 99.5

-
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: 2.498→36.73 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.35

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2198	1640	5.01 %	Random selection
R_work	0.1538	-	-	-
obs	0.1571	32804	99.78 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 45.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.498→36.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6522	0	242	215	6979

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	7023
X-RAY DIFFRACTION	f_angle_d	1.143	9576
X-RAY DIFFRACTION	f_dihedral_angle_d	16.916	4198
X-RAY DIFFRACTION	f_chiral_restr	0.061	1000
X-RAY DIFFRACTION	f_plane_restr	0.007	1291

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 (%)
2.4977-2.5349	0.3471	138	0.2571	2598	X-RAY DIFFRACTION	96
2.5349-2.5745	0.2908	138	0.2527	2590	X-RAY DIFFRACTION	100
2.5745-2.6167	0.3733	146	0.2621	2789	X-RAY DIFFRACTION	100
2.6167-2.6618	0.2758	140	0.2416	2637	X-RAY DIFFRACTION	100
2.6618-2.7102	0.3205	141	0.2193	2663	X-RAY DIFFRACTION	100
2.7102-2.7623	0.311	142	0.2203	2690	X-RAY DIFFRACTION	100
2.7623-2.8187	0.3189	145	0.202	2721	X-RAY DIFFRACTION	100
2.8187-2.88	0.2627	142	0.1878	2688	X-RAY DIFFRACTION	100
2.88-2.9469	0.2644	138	0.1816	2654	X-RAY DIFFRACTION	100
2.9469-3.0206	0.2764	144	0.1771	2685	X-RAY DIFFRACTION	100
3.0206-3.1022	0.2823	140	0.1732	2676	X-RAY DIFFRACTION	100
3.1022-3.1935	0.2323	141	0.17	2743	X-RAY DIFFRACTION	100
3.1935-3.2965	0.2423	142	0.1499	2644	X-RAY DIFFRACTION	100
3.2965-3.4142	0.268	137	0.1455	2666	X-RAY DIFFRACTION	100
3.4142-3.5508	0.1969	141	0.1433	2675	X-RAY DIFFRACTION	100
3.5508-3.7123	0.216	146	0.1332	2722	X-RAY DIFFRACTION	100
3.7123-3.9078	0.1946	141	0.132	2692	X-RAY DIFFRACTION	100
3.9078-4.1523	0.1598	143	0.1236	2699	X-RAY DIFFRACTION	100
4.1523-4.4724	0.184	139	0.1156	2635	X-RAY DIFFRACTION	100
4.4724-4.9215	0.1642	146	0.1266	2707	X-RAY DIFFRACTION	100
4.9215-5.6315	0.1991	143	0.1325	2704	X-RAY DIFFRACTION	100
5.6315-7.0867	0.1963	139	0.1349	2660	X-RAY DIFFRACTION	100
7.0867-36.7345	0.1672	141	0.1397	2683	X-RAY DIFFRACTION	99

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	0.9183	0.3945	0.036	1.5452	-0.0166	1.1037	0.2029	-0.4202	0.1293	0.0823	-0.0915	0.428	-0.1178	-0.2694	-0.0445	0.3308	0.0538	0.0478	0.6293	0.0495	0.509	78.7017	15.2068	17.1662
2	1.2023	-0.0016	0.0163	1.2472	-0.0827	0.5166	0.1688	-0.407	-0.4415	0.2549	-0.0444	0.1792	0.1516	-0.3142	-0.1096	0.4127	-0.1145	-0.0705	0.6514	0.1968	0.4553	85.1067	-8.301	21.589
3	0.7629	-0.5702	0.4461	0.4715	-0.1551	0.8815	0.0289	-0.0349	0.1585	0.0659	-0.0003	-0.0431	-0.2012	-0.042	-0.0455	0.3	-0.0519	0.0057	0.3018	0.0178	0.2675	104.2185	18.2284	14.0907
4	1.5482	-0.0313	0.3152	1.9187	0.1317	1.2872	0.019	-0.6262	0.1726	0.5208	-0.0493	0.0441	-0.3452	-0.3277	0.0073	0.3943	-0.0181	0.0043	0.5318	-0.083	0.3819	94.0862	22.3486	27.4732
5	1.2126	0.252	0.4162	2.3632	-0.23	0.9401	0.0085	0.0838	-0.0851	-0.051	0.2006	-0.0253	0.0083	-0.145	-0.1907	0.2108	-0.0222	0.0039	0.2772	0.0229	0.2832	93.9063	10.3437	9.2448
6	0.6481	-0.1651	-0.0378	0.2265	-0.0281	0.3152	0.0582	-0.0068	-0.0395	0.042	0.0828	0.0405	-0.026	-0.0774	-0.1121	0.2875	-0.0244	-0.0205	0.3456	0.0427	0.2923	97.2596	12.0176	10.14
7	0.831	-0.5603	0.2232	0.4468	-0.2027	1.017	0.0504	0.0313	-0.0028	-0.0802	-0.0365	0.1055	-0.0563	-0.1942	-0.0195	0.33	-0.0279	-0.0343	0.3527	0.0448	0.3061	89.5506	11.8212	-0.4038
8	0.7254	0.206	0.0409	1.1007	-0.3057	1.2838	-0.0594	-0.3004	-0.0033	-0.1326	0.1636	0.4557	-0.005	-0.6175	-0.0896	0.2888	0.0159	-0.0264	0.5563	0.0733	0.44	74.8442	11.2199	8.8609
9	0.5104	-0.8773	0.3185	1.5369	-0.5722	0.222	0.3611	-0.0475	-0.4492	-0.187	0.0912	0.3621	0.3151	-0.2064	-0.3274	0.3885	-0.1089	-0.1373	0.4097	-0.001	0.493	88.4574	-6.7436	5.7071
10	1.9999	2.053	-0.9537	4.3348	-1.6373	2.8171	-0.0804	0.6926	0.0275	-0.7922	0.5797	0.5236	0.3631	-0.3881	-0.4693	0.4591	-0.0935	-0.0741	0.5095	-0.0206	0.3697	104.8484	4.7253	-3.342
11	0.9889	0.1661	0.0393	1.2589	-0.2041	1.2138	0.0982	0.044	-0.139	0.0102	0.0388	-0.1856	0.0736	0.2634	-0.1112	0.2675	-0.0211	-0.032	0.3924	-0.0435	0.2983	128.795	-1.1964	19.9746
12	1.4444	0.0039	0.6371	0.6926	-0.1066	0.9309	0.1192	-0.1386	-0.2304	0.0334	0.044	-0.0632	0.1079	-0.0646	-0.1398	0.2649	-0.0312	-0.0225	0.2911	0.0112	0.2644	112.1347	-2.4102	22.1715
13	1.3764	-0.0319	0.3566	0.9368	-0.2433	1.3594	0.1341	0.1549	-0.2852	-0.031	-0.0203	-0.1527	0.2123	0.2768	-0.1168	0.2675	0.0116	-0.0229	0.3037	-0.0622	0.3496	125.1024	-8.0325	12.3266
14	2.1098	1.5834	-0.7331	4.5881	-0.9672	1.5768	0.2625	0.3667	-0.6721	-0.1225	-0.2261	-0.54	0.372	-0.0207	0.0077	0.405	-0.0582	-0.0656	0.4287	-0.0411	0.4827	106.2066	-9.8244	2.5049

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 176 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 177 through 207 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 208 through 235 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 236 through 297 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 298 through 338 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 339 through 379 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 380 through 441 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 442 through 462 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 10 through 69 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 70 through 262 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 263 through 441 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 442 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, 224 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, 224 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, 224 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