PDB-6mfy: Crystal structure of a 5-domain construct of LgrA in the substrat...

ID or keywords:

Entry

Database: PDB / ID: 6mfy

Title

Crystal structure of a 5-domain construct of LgrA in the substrate donation state

Components

Linear gramicidin synthase subunit A

Keywords

LIGASE /

nonribosomal peptide synthetase /

tailoring domain / NRPS /

enzyme /

natural product / linear gramicidin

Function / homology

Function and homology information

amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process /

phosphopantetheine binding /

ligase activity / antibiotic biosynthetic process /

cytosol
Similarity search - Function

Biological species

Brevibacillus parabrevis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Reimer, J.M. / Eivaskhani, M. / Harb, I. / Schmeing, T.M.

Funding support

Canada, 2items

Citation

Journal: Science / Year: 2019
Title: Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility.
Authors: Reimer, J.M. / Eivaskhani, M. / Harb, I. / Guarne, A. / Weigt, M. / Schmeing, T.M.

History

Deposition	Sep 12, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6mfy.cif.gz	654.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6mfy.ent.gz	536 KB	Display	PDB format
PDBx/mmJSON format	6mfy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mf/6mfy ftp://data.pdbj.org/pub/pdb/validation_reports/mf/6mfy	HTTPS FTP

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Related structure data

Related structure data	6mfwSC 6mfxC 6mfzC 6mg0C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4598 6g32-d 5wru-d 4psx-d 4qsk-d 4ax3-d 6qno-d 3l4g-3 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	#78 - Jun 2006 Luciferase similarity (6) #90 - Jun 2007 Fatty Acid Synthase similarity (6) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Linear gramicidin synthase subunit A

hetero molecules

197 kDa, 1 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)	89.863, 141.114, 171.532
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Linear gramicidin synthase subunit A Mass: 196107.047 Da / Num. of mol.: 1 / Fragment: UNP residues 2-1716 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70LM7
#2: Chemical	ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₃N₂O₇PS
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.04 Å³/Da / Density % sol: 59.57 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2 M sodium/potassium phosphate, 22% PEG3350, 0.1 M Bis-Tris propane, pH 7.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 2017
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→147.53 Å / Num. obs: 80942 / % possible obs: 99.7 % / Redundancy: 12.3 % / B_iso Wilson estimate: 50.8 Å² / R_merge(I) obs: 0.095 / Net I/σ(I): 17.4
Reflection shell	Resolution: 2.5→2.55 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4330 / CC_1/2: 0.475

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6MFW

6mfw

Resolution: 2.5→85.766 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2664	3793	5 %
R_work	0.2381	-	-
obs	0.2395	75813	99.58 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→85.766 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12694	0	71	100	12865

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	13037
X-RAY DIFFRACTION	f_angle_d	1.128	17708
X-RAY DIFFRACTION	f_dihedral_angle_d	16.682	4846
X-RAY DIFFRACTION	f_chiral_restr	0.069	1968
X-RAY DIFFRACTION	f_plane_restr	0.006	2297

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 (%)
2.5-2.5317	0.3262	124	0.3328	2345	X-RAY DIFFRACTION	89
2.5317-2.565	0.4016	138	0.3314	2637	X-RAY DIFFRACTION	100
2.565-2.6001	0.3352	140	0.3211	2639	X-RAY DIFFRACTION	100
2.6001-2.6373	0.319	138	0.3154	2651	X-RAY DIFFRACTION	100
2.6373-2.6766	0.3252	139	0.3038	2625	X-RAY DIFFRACTION	100
2.6766-2.7184	0.3234	141	0.3017	2679	X-RAY DIFFRACTION	100
2.7184-2.763	0.3143	139	0.2945	2635	X-RAY DIFFRACTION	100
2.763-2.8107	0.3238	140	0.3058	2661	X-RAY DIFFRACTION	100
2.8107-2.8618	0.3036	138	0.3007	2627	X-RAY DIFFRACTION	100
2.8618-2.9168	0.389	140	0.2995	2659	X-RAY DIFFRACTION	100
2.9168-2.9764	0.4178	141	0.3084	2663	X-RAY DIFFRACTION	100
2.9764-3.0411	0.2983	140	0.3018	2667	X-RAY DIFFRACTION	100
3.0411-3.1118	0.3542	141	0.2882	2669	X-RAY DIFFRACTION	100
3.1118-3.1897	0.3335	138	0.2764	2642	X-RAY DIFFRACTION	100
3.1897-3.2759	0.2722	141	0.2638	2674	X-RAY DIFFRACTION	100
3.2759-3.3723	0.2841	140	0.2572	2651	X-RAY DIFFRACTION	100
3.3723-3.4811	0.3098	140	0.2595	2676	X-RAY DIFFRACTION	100
3.4811-3.6056	0.2505	140	0.2343	2677	X-RAY DIFFRACTION	100
3.6056-3.7499	0.2854	143	0.2355	2682	X-RAY DIFFRACTION	100
3.7499-3.9206	0.2638	140	0.2199	2673	X-RAY DIFFRACTION	100
3.9206-4.1273	0.2435	143	0.2096	2695	X-RAY DIFFRACTION	100
4.1273-4.3859	0.2305	141	0.1959	2692	X-RAY DIFFRACTION	100
4.3859-4.7245	0.2082	143	0.1866	2699	X-RAY DIFFRACTION	100
4.7245-5.1999	0.2023	142	0.1935	2727	X-RAY DIFFRACTION	100
5.1999-5.9521	0.2715	145	0.2229	2725	X-RAY DIFFRACTION	100
5.9521-7.4984	0.2528	147	0.2249	2765	X-RAY DIFFRACTION	100
7.4984-85.8165	0.2098	151	0.205	2885	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	1.9129	-0.4448	-0.0046	2.05	1.6269	5.9997	0.0004	-0.0565	0.1745	-0.168	0.0047	-0.3143	-0.426	0.261	0.0235	0.3754	0.0225	0.0091	0.3301	0.0797	0.3951	195.0688	22.3099	35.2003
2	2.0293	-0.9229	-1.1818	2.5684	1.2364	3.4849	0.0863	0.1485	-0.0355	-0.1761	-0.0409	0.1438	-0.1058	-0.224	-0.0408	0.3376	0.0062	0.0127	0.3124	0.0078	0.2898	197.7499	-2.4911	-15.3
3	1.5228	0.91	-1.4573	1.9429	-0.4723	2.4974	-0.1462	0.5923	0.1151	-0.1896	0.0188	0.0701	0.1043	-0.4332	0.1428	0.3222	-0.022	-0.0579	0.5803	-0.0099	0.4239	175.4527	21.6129	-20.895
4	3.6049	0.9522	0.3669	4.8549	-0.068	3.8944	-0.2296	0.1621	-0.426	-0.4082	0.1154	-0.1113	0.2777	0.1214	0.158	0.6598	0.0708	0.0219	0.6522	-0.0459	0.6345	198.8249	23.9021	-37.4892
5	1.4913	-0.2427	0.1978	0.8655	0.1595	1.387	-0.0496	0.0753	0.0708	-0.07	0.0171	0.0325	-0.1178	-0.0416	0.0352	0.3233	-0.0303	-0.0082	0.3273	0.0125	0.3347	209.0014	40.8948	-16.1117
6	1.9943	-1.0291	0.2218	2.5176	-0.0108	2.0262	-0.1834	-0.153	0.8415	0.1847	0.076	0.1299	-1.3083	-0.344	0.1309	1.4263	0.2756	-0.1384	0.7489	-0.0939	1.0774	179.8188	89.4523	-13.3268

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 192 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 199 through 585 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 586 through 681 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 687 through 768 )
5	X-RAY DIFFRACTION	5	chain 'A' and ((resid 772 through 1199 ) or (resid 2000))
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1200 through 1617 )

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