PDB-4ur2: Crystal structure of the PCE reductive dehalogenase from S. multi...

ID or keywords:

Entry

Database: PDB / ID: 4ur2

Title

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

Components

TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA

Keywords

OXIDOREDUCTASE

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.096 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
Revision 1.4	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ur2.cif.gz	373.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ur2.ent.gz	304.7 KB	Display	PDB format
PDBx/mmJSON format	4ur2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ur2_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4ur2_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4ur2_validation.xml.gz	39.9 KB	Display
Data in CIF	4ur2_validation.cif.gz	58.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/4ur2 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4ur2	HTTPS FTP

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Related structure data

Related structure data	4uquC 4ur0C 4ur1C 4ur3C C: citing same article (ref.)
Similar structure data	5m8x-d 5maa-d 5m8w-d 5m2g-d 4ur3-3 5m8y-d 5m8z-d 4ur3-2 5m8u-d 5obi-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 (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

110 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)	73.243, 73.243, 184.154
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: (-0.5113, 0.0022, 0.8594), (0.0007, -1, 0.003), (0.8594, 0.0021, 0.5113)
Vector: 8.5893, -68.8969, -4.8394)

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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 , 5 types, 651 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.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 627 / 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: MERGING R VALUE FOR HIGH RESOLUTION SHELL IS 1.634
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: 1.3376
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2013 / Details: MIRRORS
Radiation	Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3376 Å / Relative weight: 1
Reflection	Resolution: 2.1→47.1 Å / Num. obs: 56502 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 27.3 % / B_iso Wilson estimate: 28.85 Å² / R_merge(I) obs: 0.24 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.1→2.17 Å / Redundancy: 26.8 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.2

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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: 2.096→47.047 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 18.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1859	2824	5 %
R_work	0.142	-	-
obs	0.1442	56502	99.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.096→47.047 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6809	0	263	627	7699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7309
X-RAY DIFFRACTION	f_angle_d	1.159	9997
X-RAY DIFFRACTION	f_dihedral_angle_d	13.469	2718
X-RAY DIFFRACTION	f_chiral_restr	0.047	1053
X-RAY DIFFRACTION	f_plane_restr	0.006	1324

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 (%)
2.0964-2.1202	0.2817	173	0.2657	3285	X-RAY DIFFRACTION	93
2.1202-2.1451	0.2517	190	0.2361	3588	X-RAY DIFFRACTION	100
2.1451-2.1713	0.2483	186	0.2139	3490	X-RAY DIFFRACTION	100
2.1713-2.1988	0.2763	190	0.2135	3597	X-RAY DIFFRACTION	100
2.1988-2.2277	0.2469	185	0.2032	3547	X-RAY DIFFRACTION	100
2.2277-2.2582	0.2471	188	0.1985	3572	X-RAY DIFFRACTION	100
2.2582-2.2905	0.2372	190	0.1866	3591	X-RAY DIFFRACTION	100
2.2905-2.3247	0.2496	183	0.1863	3483	X-RAY DIFFRACTION	100
2.3247-2.361	0.2638	189	0.1882	3637	X-RAY DIFFRACTION	100
2.361-2.3997	0.2571	185	0.1887	3494	X-RAY DIFFRACTION	100
2.3997-2.4411	0.2169	189	0.1807	3621	X-RAY DIFFRACTION	100
2.4411-2.4855	0.2349	186	0.1739	3519	X-RAY DIFFRACTION	100
2.4855-2.5333	0.2382	185	0.1708	3582	X-RAY DIFFRACTION	100
2.5333-2.585	0.2211	183	0.1643	3491	X-RAY DIFFRACTION	100
2.585-2.6412	0.219	189	0.1578	3599	X-RAY DIFFRACTION	100
2.6412-2.7026	0.2036	185	0.1493	3543	X-RAY DIFFRACTION	100
2.7026-2.7702	0.1923	187	0.1388	3543	X-RAY DIFFRACTION	100
2.7702-2.8451	0.2269	185	0.1426	3524	X-RAY DIFFRACTION	100
2.8451-2.9288	0.1929	190	0.1387	3643	X-RAY DIFFRACTION	100
2.9288-3.0233	0.188	182	0.1346	3499	X-RAY DIFFRACTION	100
3.0233-3.1314	0.1718	189	0.1252	3561	X-RAY DIFFRACTION	100
3.1314-3.2567	0.1632	185	0.1237	3547	X-RAY DIFFRACTION	100
3.2567-3.4049	0.1606	185	0.1228	3544	X-RAY DIFFRACTION	100
3.4049-3.5843	0.1628	184	0.1219	3536	X-RAY DIFFRACTION	100
3.5843-3.8088	0.1748	189	0.1187	3607	X-RAY DIFFRACTION	100
3.8088-4.1027	0.1542	186	0.1105	3559	X-RAY DIFFRACTION	100
4.1027-4.5153	0.1263	188	0.1041	3540	X-RAY DIFFRACTION	100
4.5153-5.168	0.1231	190	0.116	3554	X-RAY DIFFRACTION	100
5.168-6.5084	0.1639	185	0.1283	3563	X-RAY DIFFRACTION	100
6.5084-47.0585	0.1749	189	0.1363	3550	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	0.7393	0.0978	0.4052	2.1984	-0.2807	4.1273	0.1034	-0.2326	0.0412	0.2259	0.02	0.1977	-0.0818	-0.2669	-0.0835	0.1623	-0.0429	0.0262	0.2164	-0.0405	0.2418	-13.4684	-18.4242	5.3698
2	0.6604	0.1093	-0.0228	1.189	0.273	1.4357	-0.0175	0.0516	0.0653	-0.2046	0.0238	0.0208	-0.1967	-0.0688	-0.0124	0.2008	-0.0027	-0.0261	0.1706	-0.0189	0.1779	-7.6357	-23.76	-16.0819
3	3.2703	0.836	-0.2105	1.7168	-0.1734	2.3187	0.0243	0.125	0.0847	-0.2003	0.0295	0.238	-0.109	-0.3518	-0.0445	0.2055	0.0513	-0.0399	0.1031	-0.0577	0.2279	-16.6123	-23.3006	-16.2558
4	0.8196	0.0938	0.1015	1.22	0.1791	1.2406	0.0469	-0.1048	0.0549	0.0235	-0.0575	0.0932	-0.1065	-0.1471	0.0077	0.1633	0.0095	-0.0103	0.1894	-0.0237	0.1735	-9.6527	-23.1114	-3.8256
5	1.3709	0.1342	-0.9241	0.8782	0.2023	2.3728	0.1403	-0.1049	0.2727	0.0025	-0.0281	0.0391	-0.5079	-0.0749	-0.1199	0.3891	0.048	-0.0154	0.1776	-0.0372	0.2796	-9.3711	-3.9642	-7.2458
6	0.6384	0.5462	-0.9216	1.5518	-1.9172	2.4941	0.0269	-0.2442	0.0359	0.0249	-0.0728	-0.0868	-0.1914	0.6218	0.0629	0.2458	-0.0023	-0.0147	0.2708	-0.0446	0.2688	2.4369	-16.2636	5.0978
7	0.2307	-0.135	-0.0071	0.8944	0.4932	1.2788	0.0324	-0.4014	0.1711	0.1672	0.0305	-0.1648	-0.0998	0.3312	-0.0867	0.2415	-0.0474	-0.025	0.3211	-0.0571	0.2836	4.4637	-26.2299	3.1389
8	3.2881	0.8459	-0.4678	1.5358	-0.0933	2.1358	-0.076	-0.0968	-0.1116	0.0218	0.094	-0.364	0.4797	0.3288	-0.0698	0.3893	0.0863	-0.0425	0.1998	-0.0478	0.3687	9.4844	-56.5465	-19.6937
9	1.2253	0.101	0.1521	2.2728	1.5196	1.3143	-0.0009	-0.1192	-0.1551	0.1981	-0.017	0.2871	0.5548	-0.2558	-0.0226	0.3463	-0.0868	-0.0417	0.219	0.0255	0.2438	-14.6289	-54.6845	-8.9732
10	0.8715	0.1034	0.0298	1.2979	0.4736	1.3337	-0.0214	0.0671	-0.0101	-0.1991	0.1197	-0.2333	-0.0656	0.1323	-0.0972	0.2216	-0.0347	0.0261	0.2202	-0.0532	0.2185	7.8001	-35.7382	-25.057
11	3.8974	1.1495	-0.743	2.3876	0.6169	2.6129	-0.085	0.4824	-0.1483	-0.5235	0.1845	-0.0205	0.0454	-0.105	-0.0966	0.4002	-0.0146	-0.0261	0.2572	-0.0171	0.1986	-0.2444	-45.7321	-36.5283
12	3.2795	1.6819	-2.2917	1.8523	-0.8479	4.8834	0.045	-0.1718	-0.2054	0.0378	0.0453	-0.2706	0.2649	0.4689	-0.0996	0.1868	0.0775	-0.0269	0.1271	-0.033	0.2793	6.9315	-45.5887	-16.5742
13	0.8478	0.4535	0.0423	1.2057	0.0069	1.3334	0.0646	-0.0146	-0.2574	0.0741	0.0508	-0.3241	0.3591	0.2375	-0.0909	0.2875	0.0573	-0.0506	0.2051	-0.0652	0.3066	9.2867	-51.6444	-15.4008
14	1.0762	0.2063	-0.262	1.1655	0.132	1.5136	0.0798	-0.2457	-0.0288	0.204	0.0067	-0.1709	0.2731	0.2219	-0.0831	0.2884	0.0089	-0.0673	0.2463	-0.0081	0.2442	5.082	-43.8629	-1.5868

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 180 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 181 THROUGH 239 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 240 THROUGH 342 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 343 THROUGH 383 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 384 THROUGH 408 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 409 THROUGH 466 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 11 THROUGH 56 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 57 THROUGH 102 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 103 THROUGH 180 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 181 THROUGH 211 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 212 THROUGH 239 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 240 THROUGH 383 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 384 THROUGH 465 )

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