PDB-6bwo: LarC2, the C-terminal domain of a cyclometallase involved in the ...

ID or keywords:

Entry

Database: PDB / ID: 6bwo

Title

LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, apo form

Components

Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

Keywords

METAL BINDING PROTEIN / Lar / nickel transferase / LarC / hexamer / trimer / CTP / nickel / lactate / lactate racemization / lactate racemase

Function / homology

pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase / Nickel insertion protein / Nickel insertion protein / nickel cation binding / protein maturation / lyase activity / viral translational frameshifting / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

Function and homology information

Biological species

Lactobacillus plantarum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.03 Å

Authors

Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.

Funding support

United States, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.
Authors: Desguin, B. / Fellner, M. / Riant, O. / Hu, J. / Hausinger, R.P. / Hols, P. / Soumillion, P.

History

Deposition	Dec 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 27, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / entity_src_gen Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2	Aug 22, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 13, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6bwo.cif.gz	129.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6bwo_validation.pdf.gz	428.7 KB	Display	wwPDB validaton report
Full document	6bwo_full_validation.pdf.gz	430.9 KB	Display
Data in XML	6bwo_validation.xml.gz	13.2 KB	Display
Data in CIF	6bwo_validation.cif.gz	17.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/6bwo ftp://data.pdbj.org/pub/pdb/validation_reports/bw/6bwo	HTTPS FTP

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Related structure data

Related structure data	6bwqC 6bwrC C: citing same article (ref.)
Similar structure data	6bwr-1 6bwq-1 6usc-1 5cge-2 4wkv-d 5ifm-5 6eej-d 3b9w-1 Search similar-shape structures by Omokage search (details) 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: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

33.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

defined by author&software
Evidence: homology
101 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.900, 96.900, 96.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	B-538- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	(chain B and ((resid 272 through 273 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-ID	Component-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	chain A	A	A	272 - 415	1 - 144
2	1	ALA	ALA	(chain B and ((resid 272 through 273 and (name N...	B	B	272 - 273	1 - 2
2	2	GLN	GLN	(chain B and ((resid 272 through 273 and (name N...	B	B	272 - 415	1 - 144
2	3	GLN	GLN	(chain B and ((resid 272 through 273 and (name N...	B	B	272 - 415	1 - 144
2	4	GLN	GLN	(chain B and ((resid 272 through 273 and (name N...	B	B	272 - 415	1 - 144
2	5	GLN	GLN	(chain B and ((resid 272 through 273 and (name N...	B	B	272 - 415	1 - 144

#1: Protein	Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein / P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase ...P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase activation protein LarC / Lactate racemase maturation protein LarC / Lactate racemization operon protein LarC / Nickel-pincer cofactor biosynthesis protein LarC Mass: 16819.143 Da / Num. of mol.: 2 / Fragment: LarC2 domain of LarC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Plasmid: pET-22b_pGIR051 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: F9UST1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein / P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase ...

Mass: 16819.143 Da / Num. of mol.: 2 / Fragment: LarC2 domain of LarC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lactobacillus plantarum (bacteria) / Plasmid: pET-22b_pGIR051 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: F9UST1

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.43 % / Mosaicity: 0.14 °
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.13 ul ~13 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 0.13 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.15 M DL-Malic acid, 20% w/v Polyethylene ...Details: 0.13 ul ~13 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 0.13 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.15 M DL-Malic acid, 20% w/v Polyethylene glycol 3,350. Crystal grew within a week. The crystal was soaked for 1 minute in 25% Polyethylene glycol 400, 75% reservoir solution.

Crystal

Density Matthews: 2.25 Å³/Da / Density % sol: 45.43 % / Mosaicity: 0.14 °

Crystal grow

Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.13 ul ~13 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 0.13 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.15 M DL-Malic acid, 20% w/v Polyethylene ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.127 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.127 Å / Relative weight: 1

Reflection twin

Operator: l,-k,h / Fraction: 0.49

Reflection

Resolution: 2.03→43.33 Å / Num. obs: 19861 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC_1/2: 0.997 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.044 / R_rim(I) all: 0.112 / Net I/σ(I): 12 / Num. measured all: 124437

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.03-2.08	6.2	0.908	1440	0.553	0.395	0.992	97.8
9.07-43.33	5.8	0.039	249	0.998	0.017	0.043	97

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4.79 Å	39.56 Å
Translation	4.79 Å	39.56 Å

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Processing

Software

Name	Version	Classification
XDS	2.99	data reduction
Aimless	0.5.32	data scaling
PHASER	2.8.0	phasing
PHENIX	1.12-2829	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: in house SAD model

Resolution: 2.03→39.559 Å / Cross valid method: THROUGHOUT / σ(F): 2.37 / Phase error: 19.92

	R_factor	Num. reflection	% reflection
R_free	0.1935	3823	10.12 %
R_work	0.1395	-	-
obs	0.1519	18884	99.31 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 89.91 Å² / B_iso mean: 34.9423 Å² / B_iso min: 15.44 Å²

Refinement step

Cycle: final / Resolution: 2.03→39.559 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2280	0	0	98	2378
B_iso mean	-	-	-	38.41	-
Num. residues	-	-	-	-	288

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2320
X-RAY DIFFRACTION	f_angle_d	0.911	3155
X-RAY DIFFRACTION	f_chiral_restr	0.054	373
X-RAY DIFFRACTION	f_plane_restr	0.006	404
X-RAY DIFFRACTION	f_dihedral_angle_d	2.708	1399

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1350	X-RAY DIFFRACTION	6.711	TORSIONAL
1	2	B	1350	X-RAY DIFFRACTION	6.711	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0302-2.0652	0.2678	182	0.252	1714	1896	90
2.0652-2.1028	0.2791	193	0.2371	1735	1928	89
2.1028-2.1432	0.2953	178	0.2338	1690	1868	90
2.1432-2.187	0.2767	189	0.2212	1677	1866	89
2.187-2.2345	0.2649	182	0.2193	1703	1885	89
2.2345-2.2865	0.2482	186	0.2115	1663	1849	89
2.2865-2.3436	0.2311	185	0.1931	1689	1874	90
2.3436-2.407	0.2644	197	0.1972	1740	1937	90
2.407-2.4778	0.252	189	0.1912	1685	1874	90
2.4778-2.5578	0.2162	184	0.1818	1712	1896	90
2.5578-2.6491	0.2106	200	0.1779	1715	1915	90
2.6491-2.7552	0.2371	196	0.1703	1716	1912	90
2.7552-2.8805	0.1793	188	0.1479	1686	1874	90
2.8805-3.0323	0.1941	195	0.1454	1719	1914	90
3.0323-3.2221	0.2159	192	0.1374	1715	1907	90
3.2221-3.4707	0.1827	190	0.1213	1687	1877	90
3.4707-3.8196	0.1797	197	0.1125	1696	1893	88
3.8196-4.3713	0.1799	177	0.1053	1612	1789	86
4.3713-5.5037	0.1498	192	0.094	1717	1909	90
5.5037-34.2642	0.1913	201	0.1397	1694	1895	89

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	1.4021	-1.034	0.3974	0.8703	-1.079	5.8345	-0.0955	-0.0357	-0.0783	0.1243	0.0883	0.1181	-0.0666	-0.1623	0.0132	0.1658	-0.0324	0.0283	0.119	0.008	0.2129	34.3073	0.3441	-0.3949
2	1.2864	0.2796	0.4814	0.56	-0.6953	2.9489	0.0378	-0.2086	-0.0749	0.0912	0.0266	0.0978	0.0867	-0.1261	-0.0878	0.173	0.0151	0.0514	0.172	0.0125	0.1973	38.2255	-3.6768	4.1217
3	6.4493	-2.7002	-0.2141	3.8061	1.2029	2.7522	0.133	-0.229	-0.0162	0.4844	0.0025	0.1361	0.1061	-0.2611	-0.1343	0.3687	-0.0403	0.0301	0.3566	0.0143	0.2235	39.0105	22.497	18.6695
4	8.7571	2.8176	1.1108	9.3854	0.1784	5.7525	-0.0044	0.192	0.4884	0.0776	0.1872	0.3353	-0.0162	0.2933	-0.2029	0.2326	0.0363	0.0367	0.3573	0.0159	0.2352	28.8398	28.5405	11.9834
5	3.6009	-1.707	-0.225	2.8957	-1.0536	3.3741	-0.1285	0.2378	-0.0801	-0.0245	0.0936	0.0524	-0.2354	-0.1752	0.0229	0.2224	0.0075	0.0419	0.1906	-0.0142	0.1897	25.533	23.0972	-11.8826
6	6.5207	-0.7473	0.4892	0.6886	-0.202	0.9941	-0.0755	-0.1355	-0.0297	0.05	0.078	0.1438	-0.0385	-0.0681	0.0082	0.223	-0.0056	-0.0038	0.1562	-0.0089	0.1718	28.6433	20.5614	-6.2518
7	2.1451	2.1024	0.9157	2.5137	1.3318	1.9193	0.0414	0.0023	0.2272	0.0437	0.0045	0.3336	-0.2081	-0.087	-0.0366	0.2078	0.0308	0.0295	0.1845	0.0194	0.2534	20.8428	26.3517	-11.8579
8	2.6562	0.918	1.4547	4.3645	-3.7317	7.0902	-0.2833	-0.0122	-0.0987	0.2219	0.1089	0.2393	-0.17	-0.3533	0.1298	0.2088	0.0501	0.0462	0.2755	-0.0308	0.2672	8.235	-0.674	-11.7402
9	6.6426	0.1832	1.1218	9.0331	1.2422	4.7706	-0.0178	0.2213	0.0347	0.1576	0.0588	-0.4397	0.3665	0.1462	-0.0037	0.1817	0.01	0.034	0.2817	0.0375	0.1988	14.3298	-6.5889	-0.9519

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 272 through 316 )	A	272 - 316
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 317 through 357 )	A	317 - 357
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 358 through 387 )	A	358 - 387
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 388 through 415 )	A	388 - 415
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 272 through 287 )	B	272 - 287
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 288 through 327 )	B	288 - 327
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 328 through 357 )	B	328 - 357
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 358 through 387 )	B	358 - 387
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 388 through 415 )	B	388 - 415

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