PDB-3u9e: The crystal structure of a possible phosphate acetyl/butaryl tran...

ID or keywords:

Entry

Database: PDB / ID: 3u9e

Title

The crystal structure of a possible phosphate acetyl/butaryl transferase (from Listeria monocytogenes EGD-e) in complex with CoA.

Components

possible phosphate acetyl/butaryl transferase

Keywords

TRANSFERASE / STRUCTURAL GENOMICS / THE CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID

Function / homology

Function and homology information

acyltransferase activity
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Tan, K. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: The crystal structure of a possible phosphate acetyl/butaryl transferase (from Listeria monocytogenes EGD-e) in complex with CoA.
Authors: Tan, K. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Oct 18, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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 / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3u9e.cif.gz	238.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3u9e.ent.gz	191.7 KB	Display	PDB format
PDBx/mmJSON format	3u9e.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3u9e_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	3u9e_full_validation.pdf.gz	1.9 MB	Display
Data in XML	3u9e_validation.xml.gz	26.5 KB	Display
Data in CIF	3u9e_validation.cif.gz	35.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u9/3u9e ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u9e	HTTPS FTP

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Related structure data

Related structure data	3tngS S: Starting model for refinement
Similar structure data	6jgt-d 6jga-d 6jgg-d 6jg1-d 6p5w-d 6f57-2 6jfx-d 4om8-1 3tng-1 6jg7-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP05684

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: possible phosphate acetyl/butaryl transferase

B: possible phosphate acetyl/butaryl transferase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	43.739, 76.727, 80.090
Angle α, β, γ (deg.)	90.00, 104.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Experimentally unknown. It is predicted that the chains A and B form a dimer.

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Protein , 1 types, 2 molecules AB

#1: Protein	possible phosphate acetyl/butaryl transferase / Lmo1369 protein Mass: 31270.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo1369 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) MAGIC / References: UniProt: Q8Y7B7

#1: Protein

possible phosphate acetyl/butaryl transferase / Lmo1369 protein

Mass: 31270.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo1369 / Plasmid: PMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) MAGIC / References: UniProt: Q8Y7B7

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Non-polymers , 5 types, 178 molecules

#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.99 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis-Tris, 25% W/V PEG3350, pH 5.5, 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: 0.97926 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011 / Details: mirror
Radiation	Monochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.04→39 Å / Num. obs: 61592 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / R_merge(I) obs: 0.139 / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.685 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1607 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TNG

3tng

Resolution: 2.04→38.842 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 26.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2423	3137	5.09 %	random
R_work	0.1879	-	-	-
all	0.1908	61592	-	-
obs	0.1908	61592	95.72 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 35.518 Å² / k_sol: 0.318 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.0419 Å²	0 Å²	-5.7382 Å²
2-	-	7.0133 Å²	0 Å²
3-	-	-	-7.0552 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→38.842 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4297	0	221	158	4676

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4583
X-RAY DIFFRACTION	f_angle_d	1.064	6221
X-RAY DIFFRACTION	f_dihedral_angle_d	15.569	1678
X-RAY DIFFRACTION	f_chiral_restr	0.069	757
X-RAY DIFFRACTION	f_plane_restr	0.004	753

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 (%)
2.0398-2.0716	0.3158	141	0.2783	2279	X-RAY DIFFRACTION	81
2.0716-2.1056	0.3257	137	0.2568	2539	X-RAY DIFFRACTION	92
2.1056-2.1419	0.2633	137	0.2388	2623	X-RAY DIFFRACTION	95
2.1419-2.1809	0.2676	145	0.2514	2673	X-RAY DIFFRACTION	96
2.1809-2.2228	0.3157	131	0.2324	2647	X-RAY DIFFRACTION	97
2.2228-2.2682	0.2947	150	0.2408	2741	X-RAY DIFFRACTION	97
2.2682-2.3175	0.2917	134	0.2325	2758	X-RAY DIFFRACTION	98
2.3175-2.3714	0.2901	145	0.2289	2675	X-RAY DIFFRACTION	98
2.3714-2.4307	0.306	160	0.2186	2727	X-RAY DIFFRACTION	98
2.4307-2.4964	0.2726	153	0.2117	2682	X-RAY DIFFRACTION	98
2.4964-2.5698	0.2413	154	0.1895	2799	X-RAY DIFFRACTION	99
2.5698-2.6528	0.22	132	0.1925	2693	X-RAY DIFFRACTION	98
2.6528-2.7475	0.2775	142	0.1804	2746	X-RAY DIFFRACTION	98
2.7475-2.8575	0.2929	145	0.1878	2733	X-RAY DIFFRACTION	98
2.8575-2.9875	0.2117	136	0.1831	2700	X-RAY DIFFRACTION	98
2.9875-3.145	0.2565	131	0.1763	2784	X-RAY DIFFRACTION	99
3.145-3.3419	0.2499	149	0.1817	2697	X-RAY DIFFRACTION	98
3.3419-3.5998	0.2684	155	0.1617	2639	X-RAY DIFFRACTION	96
3.5998-3.9617	0.1991	155	0.1522	2628	X-RAY DIFFRACTION	95
3.9617-4.5342	0.1826	130	0.145	2553	X-RAY DIFFRACTION	92
4.5342-5.7097	0.1814	146	0.1616	2576	X-RAY DIFFRACTION	93
5.7097-38.8495	0.2554	129	0.2069	2563	X-RAY DIFFRACTION	91

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	2.1612	-2.1239	2.9264	2.099	-2.9639	4.5459	-0.0236	0.0888	0.3115	-0.1522	-0.7269	-0.559	-0.6787	2.3697	0.5792	0.4795	-0.0972	-0.0211	0.5734	0.0799	0.3565	11.2571	7.2313	26.4964
2	4.9383	1.2952	-0.4882	4.6853	-2.0529	3.9152	-0.0385	0.1436	-0.4682	-0.5829	-0.1883	-0.3099	0.4591	0.4609	0.2549	0.3534	0.0951	0.0293	0.3364	-0.0294	0.2146	11.2101	-10.0495	38.3393
3	1.9267	-0.7389	1.7789	2.311	-1.2184	3.8449	0.0398	-0.2069	-0.1077	0.1661	0.0599	0.2178	0.1188	-0.2539	-0.1357	0.2937	-0.0186	0.0353	0.2919	-0.0053	0.1862	-2.7435	-7.6059	42.4366
4	1.0987	-0.2283	0.8615	1.747	-0.872	3.2114	-0.0693	-0.0305	-0.0306	0.1648	0.0759	0.114	-0.1944	-0.0338	0.0065	0.1969	0.0105	0.0141	0.2122	-0.0389	0.2223	-6.8325	4.6351	23.1956
5	4.7094	0.7641	2.4421	3.981	1.7612	5.7041	-0.2456	0.0154	-0.0345	-0.1314	-0.0795	0.6386	-0.307	-0.3055	0.328	0.2071	0.0453	0.0025	0.239	0.0538	0.2797	-16.9515	9.002	15.6222
6	1.3763	-0.0266	1.1842	0.8378	-0.1372	4.7274	0.0516	-0.01	0.0768	0.0589	-0.0615	-0.0187	-0.2229	0.1839	-0.0241	0.202	-0.0128	0.0093	0.1802	-0.0182	0.2147	-3.2544	3.2868	19.4087
7	1.3964	-0.8072	2.5891	0.7566	-1.3465	4.5938	-0.0882	0.5957	0.1482	0.1017	-0.085	-0.3639	-0.1457	1.1962	0.2151	0.2795	0.0153	-0.0198	0.4479	-0.019	0.3324	-2.1498	-6.3047	-12.4953
8	2.7448	-0.8723	0.5051	2.3418	-0.7939	4.3594	-0.0381	0.3214	0.158	-0.1285	-0.004	-0.1881	-0.4228	0.3093	0.1228	0.2973	-0.0262	-0.0344	0.2123	-0.0039	0.1822	-13.6878	3.7169	-21.2821
9	1.1845	-0.9935	0.8447	1.6134	-0.7653	3.618	0.0877	0.1036	-0.1211	-0.0975	0.0238	0.1635	0.1199	-0.1508	-0.1076	0.1598	-0.0223	0.0163	0.1456	-0.0193	0.1747	-16.4876	-7.5761	-7.0716
10	1.1793	0.1261	0.2491	2.0655	-0.0922	4.3881	-0.0164	0.0048	-0.1729	0.1585	0.0424	0.1519	0.5255	-0.1622	-0.0311	0.2164	-0.0344	-0.0123	0.1293	0.0049	0.2414	-14.8523	-16.9427	7.9612
11	2.3279	0.0382	-1.2314	4.4229	-0.5162	3.7432	0.0389	-0.0949	-0.1545	0.2229	0.1292	-0.3912	0.9017	0.3723	-0.0984	0.4169	0.1163	-0.0418	0.2087	0.0319	0.2939	-3.509	-20.2075	12.8638
12	1.6951	0.2708	0.3671	1.2674	0.746	3.6416	-0.0685	0.0651	-0.0273	0.0164	0.1356	-0.0025	0.297	0.304	0.0043	0.1756	0.0511	0.0021	0.1847	-0.0011	0.224	-7.821	-7.505	3.0923
13	0.386	-0.3453	0.0282	2.6096	3.1553	4.7897	0.1713	0.2703	-0.1962	-0.0484	-0.0992	-0.154	0.4088	0.584	-0.0783	0.2	0.0777	-0.0015	0.3779	0.0258	0.2139	-6.0333	-6.9218	-11.8723

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:16)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 17:55)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 56:114)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 115:159)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 160:192)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 193:287)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 1:25)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 26:80)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 81:132)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 133:192)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 193:215)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 216:271)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 272:288)

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