PDB-4ur1: Crystal structure of the PCE reductive dehalogenase from S. multi...

ID or keywords:

Entry

Database: PDB / ID: 4ur1

Title

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

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: 1.649 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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PDBx/mmCIF format	4ur1.cif.gz	391.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ur1.ent.gz	320.2 KB	Display	PDB format
PDBx/mmJSON format	4ur1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/4ur1 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4ur1	HTTPS FTP

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Related structure data

Related structure data	4uquC 4ur0C 4ur2C 4ur3C C: citing same article (ref.)
Similar structure data	4ur3-1 4ur3-3 5m92-d 4ur2-d 4ur0-d 4uqu-d 5m8x-d 5maa-d 4ur3-2 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

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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 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)	73.703, 73.703, 185.264
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: (-0.5135, 0.0015, 0.8581), (-0.0012, -1, 0.001), (0.8581, -0.0005, 0.5135)
Vector: 7.9966, -68.6946, -4.5503)

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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, 839 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-CB0 / CIS-DIBROMOETHENE Mass: 185.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₂Br₂
#5: Chemical	ChemComp-BEN / BENZAMIDINE / Benzamidine Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₈N₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 818 / 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: 2.53 Å³/Da / Density % sol: 51.3 % / 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: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9184
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 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: 1.65→47.3 Å / Num. obs: 118228 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 27.5 % / B_iso Wilson estimate: 21.84 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 30
Reflection shell	Resolution: 1.65→1.71 Å / Redundancy: 26.2 % / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8

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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: 1.649→47.335 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 15.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1573	5911	5 %
R_work	0.1342	-	-
obs	0.1353	118227	99.84 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.649→47.335 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7001	0	305	818	8124

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7625
X-RAY DIFFRACTION	f_angle_d	1.163	10424
X-RAY DIFFRACTION	f_dihedral_angle_d	13.648	2845
X-RAY DIFFRACTION	f_chiral_restr	0.048	1090
X-RAY DIFFRACTION	f_plane_restr	0.006	1385

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 (%)
1.6487-1.6675	0.2809	373	0.2638	7060	X-RAY DIFFRACTION	95
1.6675-1.6871	0.2477	394	0.2409	7512	X-RAY DIFFRACTION	100
1.6871-1.7077	0.258	391	0.2218	7477	X-RAY DIFFRACTION	100
1.7077-1.7293	0.2274	386	0.2149	7347	X-RAY DIFFRACTION	100
1.7293-1.752	0.2375	396	0.2092	7557	X-RAY DIFFRACTION	100
1.752-1.776	0.209	382	0.1887	7317	X-RAY DIFFRACTION	100
1.776-1.8014	0.2122	402	0.1813	7582	X-RAY DIFFRACTION	100
1.8014-1.8283	0.1966	390	0.1735	7424	X-RAY DIFFRACTION	100
1.8283-1.8569	0.1956	388	0.1685	7365	X-RAY DIFFRACTION	100
1.8569-1.8873	0.1862	398	0.1606	7510	X-RAY DIFFRACTION	100
1.8873-1.9198	0.182	389	0.1509	7420	X-RAY DIFFRACTION	100
1.9198-1.9548	0.1679	393	0.1503	7462	X-RAY DIFFRACTION	100
1.9548-1.9924	0.1904	393	0.1465	7480	X-RAY DIFFRACTION	100
1.9924-2.033	0.1918	393	0.1436	7418	X-RAY DIFFRACTION	100
2.033-2.0772	0.1736	389	0.1335	7438	X-RAY DIFFRACTION	100
2.0772-2.1256	0.1557	392	0.1277	7464	X-RAY DIFFRACTION	100
2.1256-2.1787	0.1793	392	0.1293	7428	X-RAY DIFFRACTION	100
2.1787-2.2376	0.1541	396	0.127	7484	X-RAY DIFFRACTION	100
2.2376-2.3035	0.144	393	0.1248	7451	X-RAY DIFFRACTION	100
2.3035-2.3778	0.1529	386	0.1273	7421	X-RAY DIFFRACTION	100
2.3778-2.4628	0.1542	394	0.1304	7465	X-RAY DIFFRACTION	100
2.4628-2.5614	0.1724	391	0.1275	7439	X-RAY DIFFRACTION	100
2.5614-2.6779	0.1575	392	0.1301	7406	X-RAY DIFFRACTION	100
2.6779-2.8191	0.1492	393	0.1285	7485	X-RAY DIFFRACTION	100
2.8191-2.9957	0.1524	389	0.1312	7428	X-RAY DIFFRACTION	100
2.9957-3.227	0.1458	393	0.1328	7438	X-RAY DIFFRACTION	100
3.227-3.5516	0.1464	390	0.1246	7452	X-RAY DIFFRACTION	100
3.5516-4.0653	0.1346	391	0.1146	7449	X-RAY DIFFRACTION	100
4.0653-5.1209	0.1334	395	0.1096	7423	X-RAY DIFFRACTION	100
5.1209-47.3546	0.1277	393	0.1256	7455	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	0.7814	0.2454	0.8529	1.4099	-0.2626	4.3475	0.0672	-0.1752	0.0379	0.1137	-0.0249	0.0753	-0.0262	-0.265	-0.0524	0.1439	-0.0184	0.0087	0.1851	-0.0517	0.1845	-13.854	-18.4224	5.4336
2	0.4707	0.0171	0.1012	0.6533	0.1948	0.6909	-0.0205	0.049	0.05	-0.0903	0.0039	0.0361	-0.0758	-0.0631	0.0068	0.2189	-0.0042	-0.0363	0.1795	-0.0142	0.1863	-7.7876	-23.5924	-16.1511
3	2.6472	0.3774	-0.0451	1.0021	-0.2355	1.4269	-0.0179	0.0775	0.0565	-0.1293	0.0096	0.1619	-0.0418	-0.2557	0.009	0.2125	0.0298	-0.046	0.1281	-0.0499	0.199	-16.6976	-23.1777	-16.095
4	0.368	0.013	0.0217	0.3808	0.068	0.8285	-0.0069	-0.0616	0.0672	-0.002	-0.0226	0.0447	-0.1659	-0.0693	0.026	0.2192	0.0109	-0.0342	0.1776	-0.0215	0.1856	-8.1185	-17.0124	-3.3511
5	0.3794	0.0172	-0.1926	0.7696	0.2223	1.1387	-0.0186	-0.1175	0.0188	0.146	0.0374	-0.1036	-0.0746	0.0674	-0.0265	0.2106	-0.0136	-0.0496	0.1983	-0.0153	0.1963	1.3334	-20.6796	1.0876
6	2.9995	1.0729	-0.0081	1.4354	-0.0334	1.7059	-0.0576	0.0188	-0.0853	0.0071	0.0939	-0.2967	0.267	0.2111	-0.0292	0.293	0.0814	-0.0364	0.1308	-0.0309	0.2636	9.5419	-55.6837	-18.7045
7	1.1125	0.2024	-0.2549	1.8556	1.2281	1.5702	0.0082	-0.0846	-0.1255	0.1916	-0.0647	0.1489	0.4471	-0.2131	0.0736	0.3019	-0.0725	-0.045	0.1926	0.0152	0.2016	-15.0084	-54.5896	-9.0087
8	0.4446	0.0877	0.1081	0.8802	0.2475	0.8204	0.0025	0.0768	-0.0345	-0.132	0.0731	-0.1605	-0.0031	0.0857	-0.0716	0.2381	-0.0124	0.0006	0.2084	-0.0334	0.2215	7.4062	-35.6031	-25.049
9	2.4604	1.2107	-0.8273	2.1203	0.1831	2.0847	-0.1398	0.3436	-0.0582	-0.2807	0.1933	0.0029	0.1006	-0.1761	-0.0366	0.3591	-0.0304	-0.026	0.2346	-0.0162	0.1904	-0.5389	-46.0198	-36.5101
10	2.5896	1.3276	-1.5203	1.5705	-0.6093	3.2028	0.0997	-0.1869	-0.1076	0.0955	-0.045	-0.1854	0.049	0.3007	-0.0234	0.1812	0.053	-0.0453	0.0854	-0.0235	0.2118	6.5186	-45.5087	-16.5811
11	0.5907	0.2754	0.1223	1.1123	0.0373	0.8927	0.0531	-0.0134	-0.1925	0.0359	0.0365	-0.2377	0.2938	0.1542	-0.0608	0.2599	0.0442	-0.0607	0.154	-0.0343	0.2403	8.9034	-51.5395	-15.3723
12	6.2006	1.4976	-0.4613	2.6532	0.1294	1.5145	0.1478	-1.121	-0.1106	0.5264	-0.0963	-0.6635	-0.0463	0.5688	-0.0839	0.5324	-0.0338	-0.1964	0.4816	-0.0001	0.3992	12.7026	-52.5702	1.3982
13	0.7763	0.061	-0.0165	0.8129	0.0434	0.7914	0.056	-0.0807	-0.0692	0.1697	0.0164	-0.1343	0.1785	0.0978	-0.0621	0.2831	0.0086	-0.0719	0.2005	0.001	0.2379	5.7546	-45.3409	-5.4824

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 408 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 409 THROUGH 468 )
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 211 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 212 THROUGH 239 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 240 THROUGH 383 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 384 THROUGH 435 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 436 THROUGH 466 )

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