PDB-3sgt: Crystal Structure of E. coli undecaprenyl pyrophosphate synthase ...

ID or keywords:

Entry

Database: PDB / ID: 3sgt

Title

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1299

Components

Undecaprenyl pyrophosphate synthase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / Alpha/beta / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Escherichia coli O6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Cao, R. / Liu, Y.-L. / Oldfield, E.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Antibacterial drug leads targeting isoprenoid biosynthesis.
Authors: Zhu, W. / Zhang, Y. / Sinko, W. / Hensler, M.E. / Olson, J. / Molohon, K.J. / Lindert, S. / Cao, R. / Li, K. / Wang, K. / Wang, Y. / Liu, Y.L. / Sankovsky, A. / de Oliveira, C.A. / Mitchell, ...

History

Deposition	Jun 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 9, 2013	Group: Database references
Revision 1.2	Jan 16, 2013	Group: Database references
Revision 1.3	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3sgt.cif.gz	188.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3sgt.ent.gz	150.5 KB	Display	PDB format
PDBx/mmJSON format	3sgt.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/sg/3sgt ftp://data.pdbj.org/pub/pdb/validation_reports/sg/3sgt	HTTPS FTP

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Related structure data

Related structure data	3sgvSC 3sgxC 3sh0C 4h2jC 4h2mC 4h2oC 4h38C 4h3aC 4h3cC 4h8eC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cqj-d 3th8-d 3qas-d 5hxn-1 5hxo-1 4h38-d 4no5-d 3mro-d 3sgx-d 6mt4-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Undecaprenyl pyrophosphate synthase

A: Undecaprenyl pyrophosphate synthase

hetero molecules

57.3 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)	62.922, 68.351, 111.979
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Undecaprenyl pyrophosphate synthase / UPP synthase / Di-trans / poly-cis-decaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS Mass: 28481.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6 (bacteria) / Gene: uppS, c0211 / Production host: Escherichia coli (E. coli) References: UniProt: P60473, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical	ChemComp-P09 / 2-{[4-(3,4-dimethylphenoxy)phenyl]carbamoyl}benzoic acid / BPH-1299 Mass: 361.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₁₉NO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.11 Å³/Da / Density % sol: 41.81 %
Crystal grow	Temperature: 298 K / pH: 7.5 Details: 50mM HEPES, pH 7.5, 5% PEG 4,000, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 41827 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / R_merge(I) obs: 0.067 / Net I/σ(I): 41.7
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.502 / % possible all: 93.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SGV

3sgv

Resolution: 1.85→35.68 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.555 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.227	2101	5 %	RANDOM
R_work	0.174	-	-	-
obs	0.176	41639	99.2 %	-
all	-	43740	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 32.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	0 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→35.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3413	0	27	258	3698

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.021	3509
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.851	1.928	4737
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.498	5	427
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.965	23.459	185
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.279	15	584
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.175	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.161	0.2	503
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2726
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.307	1.5	2125
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.25	2	3372
X-RAY DIFFRACTION	r_scbond_it	3.559	3	1384
X-RAY DIFFRACTION	r_scangle_it	5.726	4.5	1365
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.9 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	143	-
R_work	0.228	2748	-
obs	-	-	94.2 %

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	2.0374	-1.4352	-0.5025	1.3222	0.7679	1.1264	0.0482	0.0207	-0.0807	-0.0749	-0.0557	0.0746	0.0049	0.1235	0.0074	0.116	0.0089	0.0119	0.1205	-0.0108	0.1225	19.7848	4.3556	18.5685
2	4.7208	-6.0319	-1.9436	11.5777	0.2969	1.7226	-0.2398	-0.4613	0.0054	0.1331	0.1108	-0.2337	0.145	0.4839	0.129	0.0464	0.0917	-0.0254	0.2791	-0.0053	0.1215	31.8111	-3.282	22.2739
3	0.9584	-0.6239	-0.1136	1.5402	0.1092	1.8612	0.0373	-0.0591	0.1073	-0.0269	0.0309	-0.0482	-0.1497	0.1682	-0.0682	0.1267	-0.0343	0.0141	0.1153	-0.0144	0.1158	20.7457	13.5962	22.0749
4	3.3227	0.2743	-0.8624	6.6494	0.9682	1.6852	-0.1648	-0.4266	-0.1892	-0.1444	0.3378	-0.2929	0.198	0.6848	-0.173	0.0858	0.0605	-0.0571	0.2702	-0.0134	0.1372	24.2547	6.6466	33.3398
5	1.4309	1.7921	0.9338	5.8728	0.2877	0.828	0.0328	-0.1805	0.0824	0.2323	-0.0279	-0.0534	0.0061	-0.0413	-0.0049	0.1165	-0.006	0.0024	0.1544	-0.0496	0.1291	17.0425	13.4648	33.4978
6	3.4212	-0.5769	2.4143	0.521	-1.3105	3.0535	0.0862	-0.6251	-0.233	-0.1121	0.1511	-0.0294	0.1982	-0.5012	-0.2373	0.1815	-0.0521	-0.0362	0.1945	0.0409	0.1245	16.5209	3.4713	43.1702
7	0.7928	0.5796	0.4891	1.157	0.6117	0.6153	0.0431	-0.0431	-0.0204	0.0928	0.0228	-0.0768	0.012	-0.08	-0.066	0.1239	-0.0092	-0.0001	0.1279	-0.0072	0.0994	11.1465	8.5676	31.1032
8	1.8521	0.3384	-1.5272	2.1233	-0.9224	2.2683	0.1755	-0.2109	0.3085	0.346	-0.0724	0.1393	-0.3453	0.0262	-0.1031	0.1464	-0.0155	0.0626	0.1665	-0.0684	0.1103	-10.0422	6.2833	33.7564
9	0.9359	0.3526	0.0115	0.254	0.1923	0.6689	0.0084	-0.0115	0.0395	0.0074	-0.0082	0.0323	0.0046	0.012	-0.0002	0.1191	-0.0033	0.0144	0.1074	-0.0097	0.1166	10.0426	5.6231	18.425
10	5.6042	-3.2691	1.5137	2.9413	-1.2044	1.5444	0.1242	0.1684	-0.0876	-0.5518	0.0602	0.0215	-0.228	0.2806	-0.1844	0.3293	-0.111	0.0563	0.131	-0.0106	0.0976	19.9997	12.3671	10.3449
11	0.4637	0.1924	-0.5032	0.1209	-0.035	0.6419	-0.0664	-0.0022	-0.0732	0.0509	-0.0176	-0.045	0.0555	0.0346	0.0839	0.1489	-0.0081	0.0019	0.105	0.01	0.1344	0.5123	-7.934	4.3083
12	2.9666	-3.9486	0.2554	9.5504	-5.9269	4.1568	0.1574	0.2938	0.2701	-0.2348	-0.2575	-0.3661	0.1149	0.0396	0.1	0.1287	-0.0091	-0.0318	0.1862	0.0661	0.1155	-1.2727	10.1367	-11.5
13	0.2726	-0.0143	0.072	4.8312	-2.8953	2.8941	-0.0939	0.1545	-0.0262	-0.0911	0.096	0.1663	0.1398	-0.2366	-0.0021	0.1234	-0.024	-0.0129	0.1421	-0.0134	0.1053	-6.3538	-4.2812	-5.1965
14	1.9763	-0.6661	0.6008	0.709	0.1089	0.2537	-0.0559	-0.0421	0.2857	-0.1545	-0.0122	-0.1086	-0.0499	-0.0594	0.0681	0.1934	0.0008	-0.0266	0.1445	0.0259	0.1649	-11.6951	6.3936	3.4105
15	1.642	0.8124	1.8319	5.185	0.9314	2.055	-0.0605	-0.0775	0.0264	-0.2287	-0.0257	0.3412	-0.0422	-0.0971	0.0862	0.1179	-0.0499	-0.0101	0.0897	-0.0043	0.1556	-16.7801	-10.5494	-0.1572
16	3.6384	0.1739	0.5966	4.7746	0.211	0.3435	-0.1176	-0.196	0.1164	0.2742	0.0555	0.53	0.0403	-0.2944	0.0622	0.0559	-0.0159	0.0725	0.2502	-0.0235	0.1733	-22.468	-0.3008	9.364
17	0.0953	0.1618	0.1626	0.5016	0.6824	1.4033	-0.0208	-0.0689	-0.0016	0.0287	-0.0195	0.0681	0.0625	-0.1539	0.0404	0.1128	-0.0132	0.0132	0.1376	0.0037	0.1364	-11.565	-4.5282	12.3726
18	1.8134	0.3365	-1.7573	1.6641	-0.3215	2.3147	-0.0169	-0.1115	-0.0845	0.0921	-0.0141	0.2081	0.1026	-0.0082	0.031	0.1159	-0.0277	0.0358	0.1536	0.0248	0.1012	-10.5433	-4.8689	31.7578
19	0.4115	0.1294	0.0551	0.0509	0.0534	1.0825	0.0055	-0.0173	0.0075	0.001	-0.0188	0.0186	-0.0091	0.0482	0.0133	0.1265	-0.0016	0.0118	0.1058	0.0003	0.1194	1.6229	-1.7538	8.5556
20	2.7148	-1.8948	3.147	2.3561	-1.8308	4.1261	0.0364	0.188	-0.0926	-0.0494	0.012	-0.1275	0.1761	0.1713	-0.0483	0.1499	0.0203	0.0207	0.0919	-0.0278	0.1322	7.5232	-9.8938	-0.0279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 32
2	X-RAY DIFFRACTION	2	A	33 - 49
3	X-RAY DIFFRACTION	3	A	50 - 68
4	X-RAY DIFFRACTION	4	A	69 - 100
5	X-RAY DIFFRACTION	5	A	101 - 113
6	X-RAY DIFFRACTION	6	A	114 - 127
7	X-RAY DIFFRACTION	7	A	128 - 152
8	X-RAY DIFFRACTION	8	A	153 - 177
9	X-RAY DIFFRACTION	9	A	178 - 222
10	X-RAY DIFFRACTION	10	A	223 - 239
11	X-RAY DIFFRACTION	11	B	13 - 29
12	X-RAY DIFFRACTION	12	B	30 - 37
13	X-RAY DIFFRACTION	13	B	38 - 63
14	X-RAY DIFFRACTION	14	B	64 - 92
15	X-RAY DIFFRACTION	15	B	93 - 108
16	X-RAY DIFFRACTION	16	B	109 - 128
17	X-RAY DIFFRACTION	17	B	129 - 155
18	X-RAY DIFFRACTION	18	B	156 - 181
19	X-RAY DIFFRACTION	19	B	182 - 223
20	X-RAY DIFFRACTION	20	B	224 - 240

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