PDB-5bwd: Benzylsuccinate alpha-gamma bound to fumarate

ID or keywords:

Entry

Database: PDB / ID: 5bwd

Title

Benzylsuccinate alpha-gamma bound to fumarate

Components

(benzylsuccinate synthase ...) x 2

Keywords

LYASE / complex / radical / disorder

Function / homology

Function and homology information

lyase activity
Similarity search - Function

Biological species

Thauera aromatica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Funk, M.A. / Drennan, C.L.

Funding support

United States, 2items

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation.
Authors: Funk, M.A. / Marsh, E.N. / Drennan, C.L.

History

Deposition	Jun 7, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2015	Group: Database references
Revision 1.2	Sep 23, 2015	Group: Database references
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	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
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bwd.cif.gz	375.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5bwd.ent.gz	304.4 KB	Display	PDB format
PDBx/mmJSON format	5bwd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bwd_validation.pdf.gz	483.3 KB	Display	wwPDB validaton report
Full document	5bwd_full_validation.pdf.gz	496 KB	Display
Data in XML	5bwd_validation.xml.gz	36.3 KB	Display
Data in CIF	5bwd_validation.cif.gz	51.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/5bwd ftp://data.pdbj.org/pub/pdb/validation_reports/bw/5bwd	HTTPS FTP

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Related structure data

Related structure data	5bweC 4pkcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5bwe-3 2gtq-d 3kx2-1 1c7t-d 4amw-2 2x2j-3 5bwe-2 4pkf-d 4amx-3 2x2h-4 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

Deposited unit

A: benzylsuccinate synthase alpha chain

C: benzylsuccinate synthase gamma chain

hetero molecules

107 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)	154.862, 154.862, 82.117
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

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Benzylsuccinate synthase ... , 2 types, 2 molecules AC

#1: Protein	benzylsuccinate synthase alpha chain / tutD Mass: 99117.109 Da / Num. of mol.: 1 / Mutation: M789I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutD / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68395, benzylsuccinate synthase
#2: Protein	benzylsuccinate synthase gamma chain / TutF Mass: 6865.687 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutF / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68394

#1: Protein

benzylsuccinate synthase alpha chain / tutD

Mass: 99117.109 Da / Num. of mol.: 1 / Mutation: M789I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thauera aromatica (bacteria) / Strain: T1 / Gene: tutD / Plasmid: pETDuet / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68395, benzylsuccinate synthase

#2: Protein

benzylsuccinate synthase gamma chain / TutF

Mass: 6865.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thauera aromatica (bacteria) / Strain: T1 / Gene: tutF / Plasmid: pETDuet / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68394

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Non-polymers , 5 types, 422 molecules

#3: Chemical	ChemComp-FUM / FUMARIC ACID Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₄O₄
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.22 % Description: Pale yellow and three-dimensional with rounded edges and facets. Some cabochon-like crystals with no apparent facets. Crystal morphology is pH-dependent.
Crystal grow	Temperature: 291 K / Method: vapor diffusion Details: 1:1 15 mg/mL BSS-alpha-gamma (in 20 mM HEPES, pH 7.6, 100 mM sodium chloride, 5 mM fumarate) to well solution (20% w/v PEG400, 50 mM Bis-Tris, pH 6.5, 25 mM Tris, pH 8.0) in temperature- ...Details: 1:1 15 mg/mL BSS-alpha-gamma (in 20 mM HEPES, pH 7.6, 100 mM sodium chloride, 5 mM fumarate) to well solution (20% w/v PEG400, 50 mM Bis-Tris, pH 6.5, 25 mM Tris, pH 8.0) in temperature-controlled anaerobic chamber, crystals formed in several days PH range: 6.5-8.0

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.22 %
Description: Pale yellow and three-dimensional with rounded edges and facets. Some cabochon-like crystals with no apparent facets. Crystal morphology is pH-dependent.

Crystal grow

Temperature: 291 K / Method: vapor diffusion
Details: 1:1 15 mg/mL BSS-alpha-gamma (in 20 mM HEPES, pH 7.6, 100 mM sodium chloride, 5 mM fumarate) to well solution (20% w/v PEG400, 50 mM Bis-Tris, pH 6.5, 25 mM Tris, pH 8.0) in temperature- ...
PH range: 6.5-8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→35 Å / Num. obs: 65770 / % possible obs: 97 % / Redundancy: 5.6 % / B_iso Wilson estimate: 32.19 Å² / R_sym value: 0.085 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / % possible all: 80.4

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Processing

Software

Name	Version	Classification
PHENIX	dev_1951	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4PKC

4pkc

Resolution: 2→34.628 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2232	3271	4.99 %
R_work	0.1951	-	-
obs	0.1965	65615	96.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→34.628 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7056	0	79	414	7549

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7301
X-RAY DIFFRACTION	f_angle_d	0.705	9838
X-RAY DIFFRACTION	f_dihedral_angle_d	11.984	2760
X-RAY DIFFRACTION	f_chiral_restr	0.033	1028
X-RAY DIFFRACTION	f_plane_restr	0.003	1285

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 (%)
2-2.0299	0.3997	109	0.3535	2202	X-RAY DIFFRACTION	80
2.0299-2.0616	0.3521	115	0.3126	2303	X-RAY DIFFRACTION	83
2.0616-2.0954	0.2783	129	0.3015	2373	X-RAY DIFFRACTION	87
2.0954-2.1315	0.3753	128	0.279	2487	X-RAY DIFFRACTION	90
2.1315-2.1703	0.2873	138	0.2629	2576	X-RAY DIFFRACTION	93
2.1703-2.212	0.31	144	0.2438	2718	X-RAY DIFFRACTION	99
2.212-2.2571	0.2785	145	0.222	2762	X-RAY DIFFRACTION	100
2.2571-2.3062	0.269	143	0.2053	2767	X-RAY DIFFRACTION	100
2.3062-2.3598	0.2298	148	0.202	2752	X-RAY DIFFRACTION	100
2.3598-2.4188	0.2514	147	0.2025	2769	X-RAY DIFFRACTION	100
2.4188-2.4842	0.2315	145	0.197	2770	X-RAY DIFFRACTION	100
2.4842-2.5573	0.2446	145	0.2022	2765	X-RAY DIFFRACTION	100
2.5573-2.6398	0.2269	146	0.1943	2786	X-RAY DIFFRACTION	100
2.6398-2.7341	0.2838	147	0.2029	2774	X-RAY DIFFRACTION	100
2.7341-2.8436	0.2637	146	0.2018	2780	X-RAY DIFFRACTION	100
2.8436-2.9729	0.2505	148	0.207	2798	X-RAY DIFFRACTION	100
2.9729-3.1295	0.2176	148	0.2092	2792	X-RAY DIFFRACTION	100
3.1295-3.3255	0.2513	147	0.2089	2804	X-RAY DIFFRACTION	100
3.3255-3.582	0.2067	147	0.1849	2811	X-RAY DIFFRACTION	100
3.582-3.942	0.2015	149	0.171	2819	X-RAY DIFFRACTION	100
3.942-4.5114	0.1636	149	0.1525	2841	X-RAY DIFFRACTION	100
4.5114-5.6798	0.1836	152	0.1668	2883	X-RAY DIFFRACTION	100
5.6798-34.6334	0.1877	156	0.1842	3012	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	0.456	0.1339	0.2609	0.4311	0.2171	0.1824	0.2693	0.2026	-0.271	0.0358	-0.0076	-0.3884	0.2756	0.4049	0.5413	0.3095	0.2294	-0.0524	0.5294	-0.1938	0.7367	20.2604	-62.2678	-15.0094
2	0.8677	-0.3423	0.0865	0.6156	0.0023	0.1628	-0.0075	-0.0794	-0.1546	-0.0084	0.0277	0.0421	0.0274	-0.0254	-0	0.2474	-0.0025	-0.0194	0.259	0.0162	0.2526	-12.3147	-41.6963	2.3042
3	0.2434	-0.0287	-0.1697	0.2935	-0.0957	0.1063	0.0031	0.0277	-0.0175	-0.1324	0.0355	-0.1199	0.0128	0.0465	-0	0.2721	0.0133	-0.0331	0.2915	0.0033	0.3124	3.9793	-48.2476	1.3658
4	0.397	-0.1953	0.3207	0.213	0.1704	0.633	0.0524	0.155	0.1315	-0.1039	-0.0455	-0.3927	-0.0531	0.2281	0	0.2844	0.0126	0.0623	0.3795	0.0232	0.3691	7.7912	-36.8672	-11.7799
5	0.0647	0.1201	0.0698	0.2132	0.1338	0.0711	-0.0378	0.0174	0.0721	-0.0821	-0.0053	-0.1756	-0.129	0.0005	-0	0.3254	-0.0074	0.0497	0.305	0.0564	0.2969	-7.4639	-23.4903	-19.281
6	0.2993	0.0374	0.2168	0.1012	0.0534	0.1266	0.0992	0.1344	-0.0214	-0.0723	-0.059	-0.2813	0.057	0.2004	0.0131	0.3296	0.0588	0.0569	0.3586	-0.0059	0.3748	-0.0175	-28.7699	-12.9986
7	0.0428	0.0259	-0.0178	0.0569	-0.0078	0.0038	0.0008	0.1551	-0.0265	-0.2439	-0.1492	-0.0812	-0.1325	0.0907	-0.0264	1.2469	-0.0407	0.2016	1.3006	-0.0324	0.3126	2.4864	-31.0595	-49.7893
8	0.0903	-0.1291	0.0691	0.1846	-0.096	0.0497	-0.1989	0.0607	0.0054	-0.0837	-0.0037	-0.0475	-0.0253	0.0054	-0.0179	1.1278	0.2565	0.1898	1.5933	-0.4197	0.7353	4.3386	-40.5678	-48.1252
9	0.195	0.097	-0.089	0.2842	-0.3162	0.3402	-0.1093	0.3962	0.2011	-0.1471	-0.1611	-0.4114	0.0576	0.4602	-0.4614	0.3664	0.0543	0.2524	0.6884	0.0905	0.4067	8.7369	-26.6463	-25.8786
10	0.0043	-0.0027	-0.0024	0.0054	-0.0034	0.0025	0.0154	0.0784	-0.0294	0.0656	0.0731	0.0272	0.0617	0.0899	-0.0001	0.8663	0.0894	0.1103	0.7173	-0.1626	0.4948	-0.764	-38.7904	-36.4111
11	0.0035	-0.0026	0.0016	0.0016	0.0003	0.0024	0.0413	0.0449	-0.0713	0.0216	-0.0116	0.0086	0.0217	0.0017	-0	1.0354	0.2569	-0.1577	0.9802	-0.2772	0.6707	0.7118	-43.512	-38.0171
12	0.1228	-0.0194	-0.1023	0.0346	0.0179	0.0581	-0.0187	0.4849	-0.0392	-0.1507	0.0218	-0.3044	-0.1386	0.3029	0.1209	0.6891	0.0843	0.2213	1.0887	-0.0642	0.8319	19.0181	-41.4774	-23.2013
13	0.0414	-0.0005	0.0352	0.0041	-0.011	0.0559	0.086	0.2709	0.2098	-0.0749	0.1435	-0.02	0.0449	0.102	0.0758	0.41	0.0883	0.1241	1.0365	-0.0338	0.582	25.5645	-42.8231	-15.461
14	0.4863	0.0038	0.4495	0.2619	-0.0158	0.4897	0.054	0.4659	0.0004	-0.3099	-0.2268	0.0461	0.2006	0.3414	-0.3212	0.5109	0.1464	0.0594	0.749	-0.2664	0.4341	12.7853	-51.8971	-22.4379
15	0.0158	-0.0046	-0.0258	0.0107	-0.0001	0.0651	0.0887	0.1166	-0.3335	0.0778	-0.0629	0.0094	-0.0928	0.1845	-0.0003	0.4597	0.1674	-0.0532	0.5369	-0.1767	0.5212	4.0434	-58.4957	-18.8236
16	0.0018	-0.0074	0.001	0.0165	-0.0059	0.0303	-0.002	0.167	0.1455	-0.1463	-0.1033	-0.317	-0.2304	0.2489	-0	0.8948	0.2251	-0.0329	1.2019	-0.0506	0.6344	11.587	-52.0583	-28.5578
17	0.0032	-0.0057	0.0022	0.0066	-0.0008	0.0004	0.0636	0.0692	0.1011	0.0023	-0.0051	0.0065	-0.0066	-0.0503	0	0.8043	0.2421	0.2583	1.3404	0.0731	1.4091	32.9045	-43.5813	-22.4942
18	0.0316	0.0057	-0.0016	0.0066	-0.0095	0.0084	-0.0699	0.0061	-0.1002	-0.0481	0.0084	0.2252	-0.0073	-0.4472	-0.0001	0.4486	-0.0646	0.1134	0.5229	0.1062	0.5729	-19.8211	-53.1629	20.288
19	0.0585	-0.0025	0.0546	0.0284	0.0015	0.0584	0.146	-0.0647	-0.513	-0.0861	0.2022	0.0877	0.1219	-0.1597	0.01	0.3564	0.0005	-0.0102	0.3183	0.0796	0.5975	-16.0066	-61.6679	6.9792

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 6:52)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 53:321)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 322:385)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 386:546)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 555:583)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 584:634)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 635:650)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 651:663)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 664:708)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 716:725)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 726:731)
12	X-RAY DIFFRACTION	12	chain 'A' and (resseq 744:780)
13	X-RAY DIFFRACTION	13	chain 'A' and (resseq 781:794)
14	X-RAY DIFFRACTION	14	chain 'A' and (resseq 795:815)
15	X-RAY DIFFRACTION	15	chain 'A' and (resseq 816:838)
16	X-RAY DIFFRACTION	16	chain 'A' and (resseq 839:854)
17	X-RAY DIFFRACTION	17	chain 'A' and (resseq 855:865)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 9:26)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 27:47)

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Benzylsuccinate synthase ... , 2 types, 2 molecules AC

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Non-polymers , 5 types, 422 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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-Basic information

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-Related structure data

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-Components

-Benzylsuccinate synthase ... , 2 types, 2 molecules AC

-Non-polymers , 5 types, 422 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

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+Jul 12, 2017. Major update of PDB

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Benzylsuccinate synthase ... , 2 types, 2 molecules AC

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Non-polymers , 5 types, 422 molecules

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