PDB-4gr5: Crystal structure of SlgN1deltaAsub in complex with AMPcPP

ID or keywords:

Entry

Database: PDB / ID: 4gr5

Title

Crystal structure of SlgN1deltaAsub in complex with AMPcPP

Components

Non-ribosomal peptide synthetase

Keywords

LIGASE / MbtH-like domain /

adenylation domain /

Rossmann fold /

ATP Binding

Function / homology

Function and homology information

methyltransferase activity
Similarity search - Function

Biological species

Streptomyces lydicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Herbst, D.A. / Zocher, G. / Stehle, T.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Structural Basis of the Interaction of MbtH-like Proteins, Putative Regulators of Nonribosomal Peptide Biosynthesis, with Adenylating Enzymes.
Authors: Herbst, D.A. / Boll, B. / Zocher, G. / Stehle, T. / Heide, L.

History

Deposition	Aug 24, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 12, 2012	Group: Database references
Revision 1.2	Feb 6, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.4	Jul 17, 2019	Group: Data collection / Refinement description / Category: software Item: _software.classification / _software.name / _software.version
Revision 1.5	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	4gr5.cif.gz	704.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4gr5.ent.gz	578 KB	Display	PDB format
PDBx/mmJSON format	4gr5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/4gr5 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4gr5	HTTPS FTP

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Related structure data

Related structure data	4gr4C C: citing same article (ref.)
Similar structure data	4gr4-4 4g0b-2 4gr4-1 5du9-1 3vvy-1 4gr4-3 7c6j-1 4lv7-1 4mrq-d 3op7-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4gr4C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (6) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #251 - Nov 2020 Adenylyl Cyclase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Non-ribosomal peptide synthetase

B: Non-ribosomal peptide synthetase

C: Non-ribosomal peptide synthetase

D: Non-ribosomal peptide synthetase

hetero molecules

243 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Non-ribosomal peptide synthetase

hetero molecules

defined by author&software
60.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Non-ribosomal peptide synthetase

hetero molecules

defined by author&software
60.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Non-ribosomal peptide synthetase

hetero molecules

defined by author&software
60.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Non-ribosomal peptide synthetase

hetero molecules

defined by author&software
60.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.900, 147.790, 109.920
Angle α, β, γ (deg.)	90.00, 113.06, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Non-ribosomal peptide synthetase Mass: 60109.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lydicus (bacteria) / Gene: slgN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ybdz- / References: UniProt: D1GLU5
#2: Chemical	ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1061 / 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: 2.73 Å³/Da / Density % sol: 54.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 100 mM Tris-HCl, 0.2 M Li2SO4, 1.3 M K/Na tartrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 15, 2012
Radiation	Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 1.92→47.85 Å / Num. obs: 195699 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 39.65 Å²
Reflection shell	Resolution: 1.92→2.008 Å / Mean I/σ(I) obs: 3.37 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
BUSTER	2.10.0	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.92→29.832 Å / Cor.coef. F_o:F_c: 0.9546 / Cor.coef. F_o:F_c free: 0.9498 / SU ML: 0.18 / SU R Cruickshank DPI: 0.128 / σ(F): 1.99 / Phase error: 19.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1859	5872	3 %
R_work	0.158	-	-
obs	0.1589	195699	99.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.0821 Å²	0 Å²	0.5039 Å²
2-	-	0.9877 Å²	0 Å²
3-	-	-	4.0945 Å²

Refine analyze

Luzzati coordinate error obs: 0.25 Å

Refinement step

Cycle: LAST / Resolution: 1.92→29.832 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13354	0	185	1061	14600

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	13909
X-RAY DIFFRACTION	f_angle_d	1.097	18990
X-RAY DIFFRACTION	f_dihedral_angle_d	13.214	4903
X-RAY DIFFRACTION	f_chiral_restr	0.07	2107
X-RAY DIFFRACTION	f_plane_restr	0.005	2512

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 (%)
1.92-1.9418	0.2927	195	0.2516	6307	X-RAY DIFFRACTION	99
1.9418-1.9646	0.2776	196	0.2428	6312	X-RAY DIFFRACTION	100
1.9646-1.9886	0.29	193	0.2278	6244	X-RAY DIFFRACTION	100
1.9886-2.0138	0.2568	195	0.2199	6303	X-RAY DIFFRACTION	100
2.0138-2.0403	0.2616	196	0.2072	6351	X-RAY DIFFRACTION	100
2.0403-2.0682	0.2321	195	0.2018	6294	X-RAY DIFFRACTION	100
2.0682-2.0977	0.2431	195	0.1984	6309	X-RAY DIFFRACTION	100
2.0977-2.129	0.25	195	0.1989	6309	X-RAY DIFFRACTION	100
2.129-2.1623	0.2198	195	0.1931	6298	X-RAY DIFFRACTION	100
2.1623-2.1977	0.211	197	0.1829	6383	X-RAY DIFFRACTION	100
2.1977-2.2356	0.2141	194	0.1736	6270	X-RAY DIFFRACTION	100
2.2356-2.2763	0.2178	196	0.1698	6332	X-RAY DIFFRACTION	100
2.2763-2.32	0.2128	196	0.1671	6352	X-RAY DIFFRACTION	100
2.32-2.3674	0.2255	196	0.177	6319	X-RAY DIFFRACTION	100
2.3674-2.4188	0.2169	195	0.1749	6323	X-RAY DIFFRACTION	100
2.4188-2.4751	0.2113	195	0.1709	6280	X-RAY DIFFRACTION	100
2.4751-2.5369	0.217	196	0.1716	6360	X-RAY DIFFRACTION	100
2.5369-2.6055	0.1898	197	0.1699	6361	X-RAY DIFFRACTION	100
2.6055-2.6821	0.2098	196	0.1813	6324	X-RAY DIFFRACTION	100
2.6821-2.7686	0.2495	195	0.1859	6322	X-RAY DIFFRACTION	100
2.7686-2.8675	0.2286	196	0.1894	6327	X-RAY DIFFRACTION	100
2.8675-2.9822	0.2394	196	0.1892	6338	X-RAY DIFFRACTION	100
2.9822-3.1178	0.2216	195	0.1866	6323	X-RAY DIFFRACTION	100
3.1178-3.282	0.2138	196	0.1745	6337	X-RAY DIFFRACTION	100
3.282-3.4873	0.1745	196	0.1616	6311	X-RAY DIFFRACTION	100
3.4873-3.7561	0.1776	196	0.1407	6336	X-RAY DIFFRACTION	100
3.7561-4.1332	0.1428	195	0.1267	6327	X-RAY DIFFRACTION	99
4.1332-4.7292	0.1257	197	0.1093	6358	X-RAY DIFFRACTION	99
4.7292-5.9506	0.146	197	0.1255	6377	X-RAY DIFFRACTION	100
5.9506-29.8361	0.1285	200	0.1349	6440	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	2.6704	-1.1201	-2.0512	1.4166	1.5712	3.513	0.0297	0.0783	0.1438	0.0579	-0.2036	0.2382	-0.1481	-0.5586	0.1495	0.213	-0.0116	-0.0368	0.2933	-0.0565	0.3394	-24.6866	33.0722	-24.2924
2	2.5185	0.4035	0.1834	1.9145	-0.2013	1.1766	0.0119	0.138	-0.0235	-0.1984	0.0437	0.113	0.0037	-0.1032	-0.0509	0.2259	-0.01	-0.0228	0.2306	-0.0077	0.2093	-19.2037	19.6056	-43.3983
3	0.9674	-0.342	-0.1589	1.7128	0.1929	1.4738	-0.039	-0.1397	-0.0451	0.2626	-0.0228	-0.0888	0.0904	-0.0003	0.0564	0.2223	-0.0309	-0.0332	0.2226	0.0106	0.2526	-10.1939	20.438	-20.2701
4	7.055	-0.7715	2.8646	1.0635	-1.8073	3.6451	-0.0779	-0.0341	0.0644	0.3074	0.0561	-0.5352	-0.1142	0.5795	0.045	0.399	-0.036	-0.0091	0.2989	0.0673	0.2987	20.1388	-25.3838	-1.7766
5	2.8636	-0.1089	-0.0461	2.4225	0.307	1.4922	0.0338	0.1897	-0.0474	-0.1674	-0.0618	-0.0177	0.046	0.0319	0.0256	0.228	0.0212	0.0294	0.1915	-0.0021	0.1951	3.71	-24.9179	-32.8023
6	5.2221	-0.7493	0.5739	0.6377	-0.2254	3.1263	0.1148	-0.2089	0.2839	0.0742	-0.1018	0.134	-0.0761	0.1611	-0.0264	0.3279	-0.0217	0.0435	0.1515	-0.0058	0.2596	1.4275	-23.037	-16.8587
7	1.4738	-0.4376	0.3981	1.454	0.1816	1.3747	-0.0974	-0.2829	0.0634	0.3533	0.0191	0.1844	-0.1137	-0.1524	0.0783	0.3421	0.0044	0.0641	0.2444	-0.0043	0.2666	-4.552	-14.1458	-10.5551
8	2.2284	-0.4994	-0.5912	1.8423	1.1205	2.6366	0.1004	0.4833	0.5104	-0.337	0.3085	-0.4939	-0.2011	0.6727	-0.3408	0.2789	-0.0567	0.0074	0.5443	0.025	0.3926	-30.5291	19.6631	-82.3764
9	3.1483	-0.5098	0.5662	1.8327	-0.2734	1.7857	0.0474	-0.0257	0.0098	0.1009	-0.0179	-0.0876	0.1392	0.1011	-0.0224	0.2909	-0.0007	-0.0425	0.1906	-0.0116	0.2502	-37.0749	15.8671	-62.3393
10	1.8246	-0.1456	0.1166	3.3751	0.8639	2.1406	-0.0489	0.2235	-0.0983	0.0634	-0.1285	0.3272	0.243	-0.1956	0.1853	0.2642	-0.0549	-0.0047	0.2606	-0.0116	0.3127	-54.5162	4.137	-72.1225
11	3.4993	0.8643	-0.7093	1.9436	0.4052	2.0725	-0.2669	0.7915	-0.0332	-0.6412	0.2665	0.0303	0.2035	0.0598	-0.0078	0.4486	-0.0166	-0.0668	0.4308	-0.0053	0.2182	-41.222	8.6341	-89.6416
12	3.0456	0.4534	1.0313	3.1914	1.2453	3.6488	0.1241	0.216	-0.8305	-0.4737	-0.032	0.7824	0.4001	-1.2113	-0.0699	0.4716	-0.174	-0.0977	0.7018	-0.1619	0.718	-74.052	-45.4958	-71.6194
13	2.7432	-0.8718	0.0555	2.618	-0.2195	1.9306	-0.1067	-0.1082	-0.0585	0.2315	0.0523	0.0899	-0.0537	0.0331	0.0477	0.181	0.0224	0.0249	0.1941	-0.0243	0.1849	-58.2832	-27.1001	-48.0129
14	3.0294	-3.0266	-1.3192	7.9608	0.9665	2.6515	-0.0528	-0.3175	0.1476	0.4819	0.2124	0.0558	-0.2622	-0.1321	-0.153	0.2196	-0.0122	0.05	0.2692	0.0348	0.2189	-64.1527	-27.1039	-44.399
15	1.0126	0.2713	-0.1585	2.3428	0.0324	2.1037	-0.0019	0.0751	0.0248	-0.3432	0.0043	-0.1984	-0.141	0.1756	-0.0038	0.2409	0.0119	0.0557	0.2445	-0.0202	0.2787	-48.6949	-24.9622	-66.7279
16	3.4419	0.8109	-1.2949	3.3329	0.2767	5.2107	-0.195	0.5732	-0.1853	-0.8582	-0.0077	0.1427	0.4964	-0.6332	0.1986	0.4751	0.0099	-0.0623	0.381	-0.0994	0.3004	-61.6887	-38.6285	-77.5671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 2 : 95 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 96 : 212 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 213 : 464 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 0 : 73 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 74 : 208 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 209 : 252 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 253 : 464 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 2 : 95 )
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID 96 : 240 )
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESID 241 : 346 )
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID 347 : 464 )
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESID 3 : 73 )
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESID 74 : 175 )
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESID 176 : 212 )
15	X-RAY DIFFRACTION	15	CHAIN D AND (RESID 213 : 394 )
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESID 395 : 464 )

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