PDB-4uqu: Crystal structure of the tetrachloroethene reductive dehalogenase...

ID or keywords:

Entry

Database: PDB / ID: 4uqu

Title

Crystal structure of the tetrachloroethene reductive dehalogenase from Sulfurospirillum multivorans

Components

TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA

Keywords

OXIDOREDUCTASE / ORGANOHALIDE RESPIRATION

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: 1.595 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_seq_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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	4uqu.cif.gz	378.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4uqu_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4uqu_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4uqu_validation.xml.gz	40.5 KB	Display
Data in CIF	4uqu_validation.cif.gz	60.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqu ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqu	HTTPS FTP

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Related structure data

Related structure data	4ur0C 4ur1C 4ur2C 4ur3C C: citing same article (ref.)
Similar structure data	4ur3-3 5m8w-d 5ma2-d 5m8u-d 5m8x-d 4ur0-d 5obi-d 4ur2-d 5m8y-d 5m91-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

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)	73.143, 73.143, 183.093
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: (-0.5245, 0.0002, 0.8514), (0.0006, -1, 0.0006), (0.8514, 0.0008, 0.5245)
Vector: 8.6587, -69.0091, -4.9479)

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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, 750 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.: 3 / Source method: obtained synthetically / Formula: C₇H₈N₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H₂O

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Details

Nonpolymer details	NORPSEUDO-B12 (BVQ): CCDC 217274
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: 2.49 Å³/Da / Density % sol: 50.5 % / 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 26, 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: 1.6→46.9 Å / Num. obs: 138075 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / B_iso Wilson estimate: 17.43 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.6→1.65 Å / Redundancy: 11.4 % / R_merge(I) obs: 0.98 / Mean I/σ(I) obs: 1.95 / % possible all: 96

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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: 1.595→46.861 Å / SU ML: 0.15 / σ(F): 1.38 / Phase error: 17.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.183	6332	5 %
R_work	0.1517	-	-
obs	0.1533	126646	99.59 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.595→46.861 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6923	0	261	737	7921

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7481
X-RAY DIFFRACTION	f_angle_d	1.151	10192
X-RAY DIFFRACTION	f_dihedral_angle_d	13.484	2827
X-RAY DIFFRACTION	f_chiral_restr	0.052	1077
X-RAY DIFFRACTION	f_plane_restr	0.006	1359

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 (%)
1.5951-1.6132	0.2994	184	0.2632	3501	X-RAY DIFFRACTION	88
1.6132-1.6322	0.2694	212	0.2243	4013	X-RAY DIFFRACTION	100
1.6322-1.6521	0.2617	212	0.2115	4035	X-RAY DIFFRACTION	100
1.6521-1.673	0.2455	211	0.2054	4013	X-RAY DIFFRACTION	100
1.673-1.695	0.2325	212	0.1968	4026	X-RAY DIFFRACTION	100
1.695-1.7183	0.232	212	0.1858	4019	X-RAY DIFFRACTION	100
1.7183-1.7428	0.2377	212	0.1861	4039	X-RAY DIFFRACTION	100
1.7428-1.7688	0.2199	210	0.1773	3979	X-RAY DIFFRACTION	100
1.7688-1.7965	0.2041	212	0.176	4028	X-RAY DIFFRACTION	100
1.7965-1.8259	0.2116	212	0.1723	4027	X-RAY DIFFRACTION	100
1.8259-1.8574	0.2104	212	0.1724	4038	X-RAY DIFFRACTION	100
1.8574-1.8912	0.2111	211	0.1651	4004	X-RAY DIFFRACTION	100
1.8912-1.9276	0.2151	214	0.1582	4066	X-RAY DIFFRACTION	100
1.9276-1.9669	0.1915	211	0.1547	4014	X-RAY DIFFRACTION	100
1.9669-2.0097	0.1793	209	0.1571	3975	X-RAY DIFFRACTION	100
2.0097-2.0564	0.1979	212	0.1565	4017	X-RAY DIFFRACTION	100
2.0564-2.1078	0.2049	213	0.1566	4054	X-RAY DIFFRACTION	100
2.1078-2.1648	0.1821	211	0.1545	4010	X-RAY DIFFRACTION	100
2.1648-2.2285	0.2019	213	0.1509	4035	X-RAY DIFFRACTION	100
2.2285-2.3005	0.1706	212	0.1473	4038	X-RAY DIFFRACTION	100
2.3005-2.3827	0.1957	211	0.149	4008	X-RAY DIFFRACTION	100
2.3827-2.4781	0.1818	213	0.1485	4036	X-RAY DIFFRACTION	100
2.4781-2.5909	0.1792	211	0.1501	4028	X-RAY DIFFRACTION	100
2.5909-2.7274	0.1947	214	0.1502	4054	X-RAY DIFFRACTION	100
2.7274-2.8983	0.1755	211	0.1552	4004	X-RAY DIFFRACTION	100
2.8983-3.122	0.1894	212	0.1533	4038	X-RAY DIFFRACTION	100
3.122-3.4361	0.1719	212	0.1483	4030	X-RAY DIFFRACTION	100
3.4361-3.9331	0.1621	213	0.1366	4047	X-RAY DIFFRACTION	100
3.9331-4.9545	0.1422	214	0.1257	4056	X-RAY DIFFRACTION	100
4.9545-46.8808	0.1424	214	0.127	4082	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	0.5592	-0.2148	-0.4065	1.9007	-0.1307	2.6832	-0.0321	-0.1712	0.1047	0.2347	-0.0124	0.035	-0.2501	-0.3058	0.0613	0.1321	-0.032	0.0596	0.1516	-0.0582	0.1719	-13.3285	-18.3384	5.2578
2	0.6307	0.0506	-0.1369	0.8983	0.2355	1.1881	0.0288	0.0705	0.0781	-0.1418	-0.0159	0.0004	-0.1796	-0.091	-0.0196	0.1375	0.0153	0.0068	0.1082	-0.0172	0.1289	-7.094	-23.7588	-16.2392
3	4.8075	0.6298	-1.5483	2.0692	-0.4488	3.7187	-0.0514	0.8097	0.1052	-0.3564	0.0871	0.1385	-0.1875	-0.5034	-0.0573	0.2497	0.05	-0.076	0.2713	-0.0071	0.2001	-19.0789	-20.6025	-26.3418
4	0.6755	0.275	-0.2395	1.4318	0.1517	1.2106	0.0646	-0.0493	0.0804	0.0205	-0.0443	0.0965	-0.1243	-0.1119	-0.0019	0.1038	0.0089	0.0186	0.1037	-0.0219	0.116	-10.7195	-23.3374	-5.6327
5	0.3358	0.0368	-0.7514	0.6964	-0.2071	1.7388	0.1051	-0.0377	0.1144	-0.0434	-0.0386	-0.0136	-0.3948	0.1133	-0.048	0.2358	-0.0229	0.0463	0.1268	-0.0559	0.1957	-3.4808	-9.1481	-1.4489
6	4.1108	2.7171	-1.9205	2.7602	-1.5275	2.7122	0.2625	-0.45	0.1595	0.2171	-0.1522	-0.0166	-0.1923	0.3234	-0.1214	0.1433	-0.0256	-0.0034	0.1243	-0.0461	0.1535	4.3338	-30.5808	0.3576
7	3.3586	0.693	0.0259	0.8894	0.0349	1.7509	-0.0211	-0.1113	-0.1417	-0.0171	-0.0194	-0.2314	0.3306	0.1091	0.0383	0.2745	0.0349	0.0305	0.0995	-0.0315	0.2305	9.6157	-56.6279	-19.4356
8	0.6366	0.2217	-0.1855	0.8221	0.0667	1.0133	-0.0173	0.029	-0.0939	-0.064	0.0224	-0.1003	0.175	0.0466	-0.01	0.1532	0.0034	0.0085	0.1055	-0.0343	0.139	4.6822	-47.2406	-18.8293
9	8.1284	2.4129	-0.0566	3.2498	0.3996	0.7282	0.3859	-1.2564	-0.175	0.45	-0.2574	-0.5873	0.1581	0.4048	-0.1241	0.3635	-0.0499	-0.0732	0.4313	-0.0157	0.2724	13.0838	-53.1031	1.5219
10	5.5927	2.3199	-2.0416	2.2821	-0.8743	2.6902	0.1299	-0.4633	-0.1812	0.1651	-0.1664	-0.2037	0.0832	0.3619	0.0343	0.1515	-0.0032	-0.0127	0.1355	-0.0218	0.1223	6.0011	-38.4482	-0.5743

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 201 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 202 THROUGH 342 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 343 THROUGH 435 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 436 THROUGH 466 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 11 THROUGH 56 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 57 THROUGH 383 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 384 THROUGH 435 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 436 THROUGH 465 )

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