PDB-4hn3: The crystal structure of a sex pheromone precursor (lmo1757) from...

ID or keywords:

Entry

Database: PDB / ID: 4hn3

Title

The crystal structure of a sex pheromone precursor (lmo1757) from Listeria monocytogenes EGD-e

Components

Lmo1757 protein

Keywords

SIGNALING PROTEIN / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

sex pheromone staph- cam373 precursor fold / sex pheromone staph- cam373 precursor domain / CamS sex pheromone cAM373 / CamS sex pheromone cAM373 precursor / Roll / Alpha Beta / BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / Lmo1757 protein

Function and homology information

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.047 Å

Authors

Tan, K. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: The crystal structure of a sex pheromone precursor (lmo1757) from Listeria monocytogenes EGD-e
Authors: Tan, K. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Oct 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hn3.cif.gz	541.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4hn3.ent.gz	462.8 KB	Display	PDB format
PDBx/mmJSON format	4hn3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hn3_validation.pdf.gz	494.2 KB	Display	wwPDB validaton report
Full document	4hn3_full_validation.pdf.gz	515.6 KB	Display
Data in XML	4hn3_validation.xml.gz	55.5 KB	Display
Data in CIF	4hn3_validation.cif.gz	76.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hn/4hn3 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hn3	HTTPS FTP

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Related structure data

Similar structure data	1qh4-1 1gy8-1 1i3n-d 5xjt-d 5m08-d 5nof-d 4bf2-d 6zd2-d 4lnl-d 3ftb-2 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 - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP05558

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Lmo1757 protein

B: Lmo1757 protein

C: Lmo1757 protein

D: Lmo1757 protein

hetero molecules

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

1

A: Lmo1757 protein

B: Lmo1757 protein

hetero molecules

defined by author&software
79.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Lmo1757 protein

D: Lmo1757 protein

hetero molecules

defined by author&software
79.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	149.085, 99.318, 104.608
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

Experimentally unknown. It is predicted that the chains A and B, the chain C and D form dimers, respectively.

#1: Protein	Lmo1757 protein / Sex pheromone precursor Mass: 39341.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo1757 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8Y6D1
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.46 Å³/Da / Density % sol: 50.01 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M Na2HPO4:Citric Acid, 40%(w/v) PEG300, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.05→36.1 Å / Num. all: 97717 / Num. obs: 97717 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / R_merge(I) obs: 0.076 / Net I/σ(I): 34.2
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.622 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4855 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
ARP		model building
WARP		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.047→36.013 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 23.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2207	4871	5 %	random
R_work	0.181	-	-	-
obs	0.183	97500	99.07 %	-
all	-	97500	-	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.372 Å² / k_sol: 0.354 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.2627 Å²	0 Å²	-0 Å²
2-	-	6.9089 Å²	0 Å²
3-	-	-	-5.6461 Å²

Refinement step

Cycle: LAST / Resolution: 2.047→36.013 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10381	0	145	545	11071

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10749
X-RAY DIFFRACTION	f_angle_d	0.972	14546
X-RAY DIFFRACTION	f_dihedral_angle_d	13.796	4015
X-RAY DIFFRACTION	f_chiral_restr	0.067	1583
X-RAY DIFFRACTION	f_plane_restr	0.004	1908

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 (%)
2.0466-2.0698	0.2619	149	0.2161	2981	X-RAY DIFFRACTION	95
2.0698-2.0942	0.313	182	0.2287	3024	X-RAY DIFFRACTION	100
2.0942-2.1197	0.2797	147	0.228	3087	X-RAY DIFFRACTION	100
2.1197-2.1465	0.3072	138	0.2172	3055	X-RAY DIFFRACTION	100
2.1465-2.1748	0.242	151	0.2036	3091	X-RAY DIFFRACTION	100
2.1748-2.2046	0.2811	161	0.2021	3077	X-RAY DIFFRACTION	100
2.2046-2.2361	0.2668	166	0.2034	3064	X-RAY DIFFRACTION	100
2.2361-2.2694	0.2864	171	0.2025	3073	X-RAY DIFFRACTION	100
2.2694-2.3049	0.2724	163	0.1948	3098	X-RAY DIFFRACTION	100
2.3049-2.3427	0.2279	152	0.1937	3059	X-RAY DIFFRACTION	100
2.3427-2.3831	0.2857	147	0.1942	3111	X-RAY DIFFRACTION	100
2.3831-2.4264	0.2542	170	0.2004	3078	X-RAY DIFFRACTION	100
2.4264-2.473	0.273	166	0.1932	3061	X-RAY DIFFRACTION	100
2.473-2.5235	0.2532	152	0.1988	3108	X-RAY DIFFRACTION	100
2.5235-2.5784	0.23	163	0.1908	3058	X-RAY DIFFRACTION	100
2.5784-2.6383	0.2177	165	0.1875	3089	X-RAY DIFFRACTION	100
2.6383-2.7043	0.2647	167	0.1945	3095	X-RAY DIFFRACTION	100
2.7043-2.7774	0.2461	162	0.2001	3101	X-RAY DIFFRACTION	100
2.7774-2.8591	0.2413	165	0.1927	3062	X-RAY DIFFRACTION	100
2.8591-2.9513	0.2314	165	0.1924	3111	X-RAY DIFFRACTION	100
2.9513-3.0567	0.2426	162	0.1952	3099	X-RAY DIFFRACTION	99
3.0567-3.179	0.2363	169	0.1952	3079	X-RAY DIFFRACTION	99
3.179-3.3236	0.2388	162	0.1974	3090	X-RAY DIFFRACTION	99
3.3236-3.4987	0.2432	167	0.1892	3106	X-RAY DIFFRACTION	99
3.4987-3.7177	0.2011	153	0.1726	3113	X-RAY DIFFRACTION	99
3.7177-4.0044	0.2065	157	0.1583	3128	X-RAY DIFFRACTION	99
4.0044-4.4068	0.1718	164	0.1423	3090	X-RAY DIFFRACTION	98
4.4068-5.043	0.1657	174	0.1385	3108	X-RAY DIFFRACTION	98
5.043-6.3479	0.192	176	0.1751	3127	X-RAY DIFFRACTION	98
6.3479-36.0185	0.2013	185	0.1901	3206	X-RAY DIFFRACTION	96

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	1.4949	0.2545	-0.6946	1.8745	-0.4292	2.1608	0.0503	0.0646	0.1089	-0.0552	0.0311	0.0126	0.0326	0.0857	-0.0491	0.1222	0.0263	-0.0022	0.176	-0.0083	0.1571	110.4147	20.1049	77.1864
2	5.2817	-2.6427	-3.2402	3.0504	1.5793	4.2168	-0.0754	0.0367	-0.1798	0.1546	0.0669	0.2074	0.1369	-0.1565	-0.0142	0.23	-0.0183	-0.0125	0.1642	-0.0071	0.1544	96.6816	14.4164	100.1446
3	1.8832	-0.1187	-0.4523	2.4602	0.4945	2.7794	-0.3447	-0.3787	-0.3337	0.452	0.1189	0.391	0.4457	0.0319	0.093	0.3409	0.0662	0.1816	0.2878	0.0354	0.2756	74.7289	21.6045	112.5272
4	2.2424	-0.0323	-0.5804	2.2661	0.1875	1.0844	-0.1406	-0.2468	0.0167	0.1423	-0.0356	0.2818	0.0866	-0.1431	0.0109	0.2187	0.0668	0.0651	0.1957	-0.0203	0.1169	74.7575	35.8477	109.1771
5	5.1348	-1.8616	-3.3956	2.4646	2.4854	3.3031	0.0841	-0.1989	0.4739	-0.0696	0.2116	-0.2495	-0.1323	0.2302	-0.2354	0.1734	0.0073	-0.0039	0.2127	-0.0039	0.2183	97.8711	34.5434	97.8795
6	2.6597	-0.2655	-0.4939	2.29	-0.1142	3.1967	0.0209	0.0595	0.4266	0.1118	0.0035	0.125	-0.3949	-0.2742	-0.0031	0.1626	0.0001	0.0384	0.1298	-0.0397	0.2565	40.4754	30.7473	79.6486
7	1.1088	-0.3246	-0.3205	2.5421	0.6082	2.9806	0.0533	-0.1195	-0.0002	0.1553	-0.0314	0.2583	0.2202	-0.2529	-0.0118	0.1984	-0.0575	0.0061	0.2026	0.0264	0.237	41.3226	16.2426	79.3651
8	4.0557	2.3161	-1.7418	2.6707	-0.9954	4.1321	0.1213	0.0438	-0.053	0.0128	-0.0371	-0.1373	0.1957	0.3059	-0.1174	0.2014	0.0376	-0.0412	0.1628	0.0245	0.1322	54.4584	16.3843	56.7573
9	1.599	0.1484	-0.4274	1.8236	0.5844	2.2873	0.1263	-0.1558	-0.0004	-0.0279	0.2203	-0.4248	-0.1549	0.5426	-0.1447	0.0786	-0.079	0.0558	0.4575	-0.0959	0.1325	79.9	23.6534	45.3031
10	2.4756	-0.4421	-0.7211	4.3425	1.4422	2.063	0.1484	0.1432	0.5764	-0.3182	0.1523	0.1541	-0.5537	0.2935	-0.2583	0.3821	-0.1637	0.0864	0.3453	0.0469	0.361	72.2076	37.8588	47.1164
11	4.4922	1.2518	-3.2393	3.385	-1.1834	3.4977	0.2757	0.2499	0.8387	0.0817	0.1349	0.3025	-0.5763	-0.0495	-0.3355	0.2618	-0.0194	0.0191	0.214	0.0669	0.3587	55.4482	36.3577	59.3484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 40:286)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 287:371)
3	X-RAY DIFFRACTION	3	chain 'B' and (resseq 38:169)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 170:286)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 287:371)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 41:160)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 161:286)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 287:371)
9	X-RAY DIFFRACTION	9	chain 'D' and (resseq 39:209)
10	X-RAY DIFFRACTION	10	chain 'D' and (resseq 210:286)
11	X-RAY DIFFRACTION	11	chain 'D' and (resseq 287:371)

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