PDB-3uf6: The crystal structure of a possible phosphate acetyl/butaryl tran...

ID or keywords:

Entry

Database: PDB / ID: 3uf6

Title

The crystal structure of a possible phosphate acetyl/butaryl transferase (from Listeria monocytogenes EGD-e) in complex with CoD (3'-dephosphocoenzyme A)

Components

Lmo1369 protein

Keywords

TRANSFERASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / Unknown Function

Function / homology

Function and homology information

acyltransferase activity
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Tan, K. / Zhou, 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 possible phosphate acetyl/butaryl transferase (from Listeria monocytogenes EGD-e) in complex with CoD (3'-dephosphocoenzyme A)
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Oct 31, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3uf6.cif.gz	234.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3uf6.ent.gz	189.2 KB	Display	PDB format
PDBx/mmJSON format	3uf6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3uf6_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3uf6_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3uf6_validation.xml.gz	26.7 KB	Display
Data in CIF	3uf6_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/3uf6 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/3uf6	HTTPS FTP

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Related structure data

Related structure data	3tngS 3u9e S: Starting model for refinement
Similar structure data	3tng-1 2i4t-d 4mw1-1 1rz5-2 1pwe-7 3ozp-d 1pwe-8 1bf2-d 3u9e-d 5xc2-1 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

Deposited unit

A: Lmo1369 protein

B: Lmo1369 protein

hetero molecules

63.9 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)	53.440, 75.594, 60.332
Angle α, β, γ (deg.)	90.00, 91.62, 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.

#1: Protein	Lmo1369 protein / possible phosphate acetyl/butaryl transferase 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) majic / References: UniProt: Q8Y7B7
#2: Chemical	ChemComp-COD / DEPHOSPHO COENZYME A Mass: 687.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₅N₇O₁₃P₂S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 371 / 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: 1.95 Å³/Da / Density % sol: 36.85 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M ammonium Acetate, 0.1M Bis-Tris, 25% w/v PEG 3350, 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: 1.8→32 Å / Num. all: 44398 / Num. obs: 44398 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / R_merge(I) obs: 0.101 / Net I/σ(I): 16.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 2.64 / Num. unique all: 2203 / % possible all: 99.2

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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-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TNG

3tng

Resolution: 1.8→32 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 19.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2094	2234	5.04 %	random
R_work	0.1638	-	-	-
all	0.1661	44366	-	-
obs	0.1661	44366	99.49 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.835 Å² / k_sol: 0.37 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.8534 Å²	-0 Å²	3.0448 Å²
2-	-	-1.0865 Å²	-0 Å²
3-	-	-	0.2331 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4289	0	54	371	4714

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4474
X-RAY DIFFRACTION	f_angle_d	1.057	6103
X-RAY DIFFRACTION	f_dihedral_angle_d	12.733	1647
X-RAY DIFFRACTION	f_chiral_restr	0.073	761
X-RAY DIFFRACTION	f_plane_restr	0.004	762

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 (%)
1.7991-1.8382	0.2903	120	0.214	2573	X-RAY DIFFRACTION	97
1.8382-1.8809	0.2545	131	0.1994	2609	X-RAY DIFFRACTION	99
1.8809-1.928	0.2702	149	0.1777	2617	X-RAY DIFFRACTION	99
1.928-1.9801	0.2106	144	0.1712	2646	X-RAY DIFFRACTION	100
1.9801-2.0383	0.2072	133	0.1579	2616	X-RAY DIFFRACTION	100
2.0383-2.1041	0.2318	130	0.1716	2653	X-RAY DIFFRACTION	100
2.1041-2.1793	0.2263	157	0.1652	2584	X-RAY DIFFRACTION	100
2.1793-2.2665	0.2318	156	0.1559	2618	X-RAY DIFFRACTION	100
2.2665-2.3697	0.1946	138	0.1597	2647	X-RAY DIFFRACTION	100
2.3697-2.4945	0.2428	134	0.1654	2634	X-RAY DIFFRACTION	100
2.4945-2.6508	0.2394	135	0.1838	2662	X-RAY DIFFRACTION	100
2.6508-2.8553	0.2573	149	0.1843	2631	X-RAY DIFFRACTION	100
2.8553-3.1424	0.1989	126	0.171	2672	X-RAY DIFFRACTION	100
3.1424-3.5966	0.1778	134	0.1523	2643	X-RAY DIFFRACTION	100
3.5966-4.5293	0.1605	149	0.1346	2653	X-RAY DIFFRACTION	100
4.5293-32.0319	0.1863	149	0.1584	2674	X-RAY DIFFRACTION	99

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	1.6117	-0.3439	-0.4108	1.2257	0.2857	1.4808	-0.0218	0.2772	-0.0232	-0.3836	-0.0039	0.1336	-0.11	-0.0681	0.0318	0.1127	-0.0216	-0.034	0.0905	0.0055	0.0741	-24.9703	33.4533	56.3039
2	2.0886	-0.1532	0.8665	2.004	1.2014	3.6924	-0.074	0.0258	0.289	-0.2455	-0.1299	0.4037	-0.467	-0.3491	0.1	0.0819	0.0258	-0.0248	0.1134	0.0034	0.1474	-30.0411	41.3863	65.1574
3	0.7691	-0.0695	-0.5755	0.7272	0.2691	0.96	-0.0389	-0.1525	-0.0004	0.126	0.0108	0.0422	0.0009	0.1829	-0.0139	0.0208	-0.012	-0.018	0.08	0.0092	0.0522	-15.4001	34.636	66.4171
4	3.1252	1.0902	1.2037	3.2484	0.3373	2.2633	0.0352	-0.1585	0.0003	0.1531	-0.0603	0.0076	0.0414	0.1051	0.0075	0.0713	0.0295	0.0172	0.1193	0.0343	0.0319	-2.2879	25.5549	60.8267
5	2.6193	0.1408	-0.4122	1.7874	-0.8305	1.5207	-0.2227	-0.168	-0.2303	-0.0397	-0.0154	-0.2173	0.1515	0.0954	0.199	0.1077	0.0486	0.0212	0.0586	0.007	0.0855	7.112	20.8987	52.8374
6	3.1445	0.1465	0.1708	2.3479	0.1383	1.3522	-0.0705	-0.12	-0.401	-0.0025	0.0488	0.0142	0.4712	-0.0146	-0.0745	0.1689	0.0258	0.0342	0.075	-0.0019	0.1581	2.8249	17.2817	44.4492
7	1.4718	-0.2041	-0.6815	0.1296	-0.3535	2.296	-0.1173	0.0861	-0.3865	-0.1251	-0.0192	-0.0303	0.5351	0.0096	0.0351	0.1436	0.0181	0.0173	0.0637	0.0077	0.1395	0.3005	19.0624	47
8	1.2162	-0.0387	-0.757	0.3989	-0.5019	3.1385	0.0408	-0.037	0.1106	-0.0052	0.0331	0.0138	-0.0664	-0.1937	-0.0668	0.0492	0.0067	-0.0054	0.0623	-0.005	0.0459	-9.9685	34.9682	53.0793
9	5.9782	-1.4509	1.212	2.5187	-0.3004	4.8242	-0.053	0.1709	0.0269	-0.16	0.0541	0.148	0.0367	-0.0682	-0.0503	-0.0092	-0.0197	-0.0067	0.0725	-0.0059	0.0297	-20.3665	29.9552	56.2788
10	0.5365	-0.0364	-0.8181	1.0088	0.5317	1.4732	0.0156	0.2013	-0.0121	-0.1225	-0.0382	0.2529	-0.0676	-0.3915	0.0111	0.0156	-0.0541	0.0097	0.0953	0.0032	0.0725	8.4636	32.6171	20.2414
11	4.3959	-1.2614	0.5492	2.8139	0.2776	1.8307	0.1444	0.1169	-0.4499	-0.2361	-0.0382	0.1511	0.1873	-0.1014	-0.0646	0.1046	-0.0411	0.0147	0.1035	-0.036	0.0761	18.0733	25.6302	15.3372
12	3.3144	-0.1631	0.6691	3.0857	-0.2212	3.7536	0.096	-0.1086	-0.3151	0.0943	0.0014	-0.1151	0.1737	0.2494	-0.0631	0.0473	0.0011	0.0471	0.0554	-0.0082	0.0575	26.2761	27.7357	20.0696
13	0.6828	-0.2157	-0.6809	0.7727	0.5765	1.0283	0.0494	-0.2294	0.1142	0.1218	0.0509	-0.3084	-0.0137	0.2059	-0.0057	0.0531	-0.0313	-0.0077	0.1127	0.0091	0.1504	25.1485	35.4376	31.3561
14	1.3132	0.3983	-0.0145	1.3217	0.5202	1.5343	0.018	-0.0853	0.1046	0.0799	0.0195	-0.0391	-0.068	0.0141	-0.0276	0.0635	0.012	0.0035	0.0453	-0.0042	0.0647	6.8649	46.5351	43.1092
15	2.3084	-0.0955	-0.2362	1.0172	-0.3618	0.5835	-0.083	-0.0322	0.3629	0.2047	0.1027	0.2113	-0.3454	-0.303	-0.084	0.1	0.1044	0.0052	0.0829	-0.0007	0.0812	-4.8988	48.1575	44.5257
16	1.8153	0.68	-1.0044	1.0295	-0.049	1.4295	-0.1598	0.0933	-0.1663	-0.0308	0.1103	-0.0553	0.0552	0.0719	0.0592	0.0473	0.0038	0.0069	0.0592	-0.0085	0.0704	7.2929	32.5727	35.1512
17	6.471	2.4005	-0.9248	4.4291	1.7952	4.208	-0.0673	0.3778	0.1497	-0.2904	0.0292	0.0744	-0.0866	-0.2518	-0.108	0.0229	0.0051	0.0144	0.114	0.0007	0.0258	8.774	36.2677	23.9884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:38)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 39:55)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 56:132)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 133:159)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 160:192)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 193:216)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 217:233)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 234:271)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 272:287)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 2:37)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 38:55)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 56:80)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 81:114)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 115:203)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 204:233)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 234:271)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 272:287)

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