PDB-4ur0: Crystal structure of the PCE reductive dehalogenase from S. multi...

ID or keywords:

Entry

Database: PDB / ID: 4ur0

Title

Crystal structure of the PCE reductive dehalogenase from S. multivorans in complex with trichloroethene

Components

TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA

Keywords

OXIDOREDUCTASE

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.798 Å

Authors

Bommer, M. / Kunze, C. / Fesseler, J. / Schubert, T. / Diekert, G. / Dobbek, H.

Citation

Journal: Science / Year: 2014
Title: Structural Basis for Organohalide Respiration.
Authors: Bommer, M. / Kunze, C. / Fesseler, J. / Schubert, T. / Diekert, G. / Dobbek, H.

History

Deposition	Jun 25, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 5, 2014	Group: Database references
Revision 1.2	Jul 12, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Mar 6, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ur0.cif.gz	382.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ur0.ent.gz	326.5 KB	Display	PDB format
PDBx/mmJSON format	4ur0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/4ur0 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4ur0	HTTPS FTP

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Related structure data

Related structure data	4uquC 4ur1C 4ur2C 4ur3C C: citing same article (ref.)
Similar structure data	4ur3-3 4uqu-d 5m8w-d 4ur1-d 5m8x-d 4ur3-1 4ur2-d 5m8y-d 5obi-d 5m8z-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 (14) #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 (14)
#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 author&software

Unit cell

Length a, b, c (Å)	73.956, 73.956, 185.421
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.5114, 0.0011, 0.8594), (-0.0012, -1, 0.0006), (0.8594, -0.0007, 0.5114)
Vector: 7.9387, -69.0633, -4.5371)

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Protein , 1 types, 2 molecules AB

#1: Protein	TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA / PCE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA Mass: 52164.387 Da / Num. of mol.: 2 / Fragment: RESIDUES 38-501 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) 12446 / Source: (natural) SULFUROSPIRILLUM MULTIVORANS (bacteria) / References: UniProt: W6EQP0, EC: 1.97.1.8

#1: Protein

TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA / PCE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA

Mass: 52164.387 Da / Num. of mol.: 2 / Fragment: RESIDUES 38-501 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) 12446 / Source: (natural)

SULFUROSPIRILLUM MULTIVORANS (bacteria) / References: UniProt: W6EQP0, EC: 1.97.1.8

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Non-polymers , 6 types, 824 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-BVQ / NORPSEUDO-B12 Mass: 1305.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅₇H₈₂CoN₁₆O₁₄P
#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.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-TCV / 1,1,2-trichloroethene / Trichloroethylene Mass: 131.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂HCl₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	THE DATA BASE ENTRY CONTAINS A SIGNAL PEPTIDE (AA 1-37) NOT PRESENT IN THE MATURE PEPTIDE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.7 % / Description: NONE
Crystal grow	Method: vapor diffusion / pH: 8 Details: VAPOUR DIFFUSION UNDER ANAEROBIC CONDITIONS (95% N2 / 5% H2), 50 MM TRIS-HCL PH 8.0, 15% PEG 3350, 0.2 M NAMALONATE, 2% BENZAMIDINE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013 / Details: MIRRORS
Radiation	Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.8→45.5 Å / Num. obs: 91944 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.8 % / B_iso Wilson estimate: 20.14 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 16
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 12.3 % / R_merge(I) obs: 1.25 / Mean I/σ(I) obs: 1.93 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.798→45.548 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 16.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1649	4598	5 %
R_work	0.1359	-	-
obs	0.1374	91941	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 26.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.798→45.548 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7001	0	278	807	8086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7604
X-RAY DIFFRACTION	f_angle_d	1.117	10401
X-RAY DIFFRACTION	f_dihedral_angle_d	13.166	2837
X-RAY DIFFRACTION	f_chiral_restr	0.047	1090
X-RAY DIFFRACTION	f_plane_restr	0.005	1381

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 (%)
1.7979-1.8183	0.2616	149	0.2305	2819	X-RAY DIFFRACTION	98
1.8183-1.8397	0.2454	154	0.2121	2940	X-RAY DIFFRACTION	100
1.8397-1.8621	0.2263	152	0.2076	2876	X-RAY DIFFRACTION	100
1.8621-1.8857	0.2536	152	0.2	2884	X-RAY DIFFRACTION	100
1.8857-1.9105	0.2281	153	0.1936	2911	X-RAY DIFFRACTION	100
1.9105-1.9367	0.2395	154	0.1844	2935	X-RAY DIFFRACTION	100
1.9367-1.9644	0.2006	153	0.1713	2896	X-RAY DIFFRACTION	100
1.9644-1.9937	0.1905	156	0.1644	2962	X-RAY DIFFRACTION	100
1.9937-2.0248	0.2533	149	0.1627	2844	X-RAY DIFFRACTION	100
2.0248-2.058	0.189	156	0.1536	2960	X-RAY DIFFRACTION	100
2.058-2.0935	0.1958	152	0.1466	2890	X-RAY DIFFRACTION	100
2.0935-2.1316	0.1766	153	0.146	2906	X-RAY DIFFRACTION	100
2.1316-2.1726	0.1836	155	0.1371	2943	X-RAY DIFFRACTION	100
2.1726-2.2169	0.1803	151	0.1371	2860	X-RAY DIFFRACTION	100
2.2169-2.2651	0.1793	153	0.1394	2917	X-RAY DIFFRACTION	100
2.2651-2.3178	0.1592	154	0.1329	2921	X-RAY DIFFRACTION	100
2.3178-2.3758	0.2016	153	0.1321	2902	X-RAY DIFFRACTION	100
2.3758-2.44	0.1631	154	0.1328	2926	X-RAY DIFFRACTION	100
2.44-2.5118	0.1624	152	0.1338	2901	X-RAY DIFFRACTION	100
2.5118-2.5929	0.1793	154	0.1319	2919	X-RAY DIFFRACTION	100
2.5929-2.6855	0.1726	153	0.1344	2907	X-RAY DIFFRACTION	100
2.6855-2.793	0.1587	153	0.1333	2917	X-RAY DIFFRACTION	100
2.793-2.9201	0.1976	154	0.1394	2925	X-RAY DIFFRACTION	100
2.9201-3.0741	0.1637	155	0.1389	2929	X-RAY DIFFRACTION	100
3.0741-3.2666	0.1674	152	0.137	2896	X-RAY DIFFRACTION	100
3.2666-3.5187	0.1398	154	0.1318	2925	X-RAY DIFFRACTION	100
3.5187-3.8727	0.1331	155	0.1158	2942	X-RAY DIFFRACTION	100
3.8727-4.4327	0.113	152	0.1023	2902	X-RAY DIFFRACTION	100
4.4327-5.5831	0.1271	155	0.1102	2937	X-RAY DIFFRACTION	100
5.5831-45.563	0.1381	156	0.1231	2951	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	1.0334	0.0334	0.4241	0.8104	-0.4179	3.9471	0.062	-0.1578	0.0829	0.0468	0.0299	0.1251	-0.0237	-0.36	-0.0963	0.1258	-0.0135	-0.0109	0.122	-0.0483	0.1619	-16.0165	-16.6519	1.5786
2	0.5529	0.1584	0.0441	0.7412	0.1266	0.6522	-0.0382	0.0598	0.0425	-0.0817	0.0302	0.0487	-0.0332	-0.0753	0.0011	0.1716	-0.0086	-0.0305	0.1509	-0.011	0.1451	-10.1201	-23.7714	-16.033
3	0.7376	0.2659	0.0948	0.7011	0.1703	0.965	-0.0112	-0.0604	0.0618	0.0314	-0.0064	0.0688	-0.0494	-0.0858	0.0175	0.1505	0.0077	-0.0244	0.1411	-0.0143	0.134	-10.1095	-22.1785	-3.3469
4	0.4372	0.1177	-0.4756	0.3426	0.1908	1.4218	-0.0047	-0.1026	0.0843	0.0346	0.013	-0.0182	-0.2295	0.1007	0.0184	0.2025	-0.0137	-0.0359	0.136	-0.0288	0.1852	-2.331	-9.7737	-0.2662
5	0.4308	0.1088	-0.0114	0.9881	0.1803	0.6479	-0.0199	-0.0532	-0.0394	0.1516	0.0317	-0.0869	0.0616	0.0072	0.0094	0.1573	-0.0033	-0.0316	0.1208	-0.0135	0.1327	-1.5598	-24.1414	-1.3858
6	2.9463	1.0104	-0.0525	1.3259	0.0434	1.5046	-0.0743	0.0842	-0.1799	-0.0118	0.106	-0.2704	0.3285	0.1325	-0.0099	0.3197	0.0629	-0.0395	0.1126	-0.024	0.2198	6.9268	-57.4351	-20.3194
7	1.5386	0.2642	-0.6488	1.7567	0.7571	2.1207	-0.0017	-0.094	-0.0991	0.2243	-0.0313	0.1496	0.4577	-0.1699	0.0753	0.273	-0.0555	-0.0501	0.1511	0.008	0.1669	-14.5125	-53.37	-8.9289
8	0.6456	0.1098	0.1921	1.3285	0.2628	0.8838	-0.0296	0.0952	-0.0288	-0.1646	0.1117	-0.1822	0.0199	0.1091	-0.084	0.1954	-0.0123	0.0179	0.172	-0.0332	0.164	7.5242	-35.4945	-25.8375
9	2.0072	0.9003	-0.8588	1.2404	-0.0589	2.3349	-0.0936	0.163	-0.061	-0.1219	0.1156	-0.0935	0.1682	0.047	-0.0089	0.21	0.0342	-0.0249	0.0552	-0.0279	0.1741	2.6464	-46.3971	-25.5939
10	0.7711	0.333	-0.0101	1.3068	-0.0935	1.0786	0.0785	-0.1107	-0.1827	0.1375	0.0117	-0.3011	0.3436	0.2251	-0.0622	0.291	0.0537	-0.0799	0.1799	-0.0344	0.2457	9.5195	-51.9347	-12.0417
11	0.7078	0.0253	-0.1101	0.7945	0.032	0.5371	0.0511	-0.1049	-0.016	0.1855	0.0364	-0.1395	0.1409	0.1037	-0.1024	0.2358	0.0199	-0.0701	0.1362	-0.0165	0.1885	7.0222	-45.1923	-6.367

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 5 THROUGH 39 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 40 THROUGH 239 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 240 THROUGH 342 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 343 THROUGH 435 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 436 THROUGH 466 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 9 THROUGH 56 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 57 THROUGH 102 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 103 THROUGH 180 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 181 THROUGH 239 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 240 THROUGH 435 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 436 THROUGH 465 )

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