PDB-3sh0: Crystal Structure of E. coli undecaprenyl pyrophosphate synthase ...

ID or keywords:

Entry

Database: PDB / ID: 3sh0

Title

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1065

Components

Undecaprenyl pyrophosphate synthase

Keywords

TRANSFERASE/TRANSFERASE Inhibitor / Alpha/beta / TRANSFERASE-TRANSFERASE Inhibitor complex

Function / homology

Function and homology information

Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 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 16, 2013	Group: Database references
Revision 1.2	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

-
Download

PDBx/mmCIF format	3sh0.cif.gz	191.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3sh0.ent.gz	152.6 KB	Display	PDB format
PDBx/mmJSON format	3sh0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3sh0_validation.pdf.gz	843.8 KB	Display	wwPDB validaton report
Full document	3sh0_full_validation.pdf.gz	852.7 KB	Display
Data in XML	3sh0_validation.xml.gz	22.7 KB	Display
Data in CIF	3sh0_validation.cif.gz	32.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sh/3sh0 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3sh0	HTTPS FTP

-
Related structure data

Related structure data	3sgtC 3sgvC 3sgxC 4h2jC 4h2mC 4h2oC 4h38C 4h3aC 4h3cC 4h8eC 2e98S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2e9c-d 3qas-d 3sgx-d 4h38-d 4h2j-d 4h2m-d 4h3c-d 5cqj-d 3sju-d 2e9d-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Undecaprenyl pyrophosphate synthase

A: Undecaprenyl pyrophosphate synthase

hetero molecules

57.9 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)	62.765, 68.724, 112.056
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 (E. coli) / Strain: K12 / Gene: uppS, ispU, rth, yaeS, b0174, JW0169 / Production host: Escherichia coli (E. coli) References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical	ChemComp-SAX / 2-(dodecyloxy)-6-hydroxybenzoic acid Mass: 322.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₉H₃₀O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM HEPES, pH 7.5, 5% PEG 4,000, vapor diffusion, hanging drop, temperature 298K

-
Data collection

Diffraction

Mean temperature: 298 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 0.9787 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2010

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 1.84→50 Å / Num. obs: 42560 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10 % / R_merge(I) obs: 0.065 / Χ²: 0.737 / Net I/σ(I): 8.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.84-1.87	5.3	0.642	1870	0.512	1	89.2
1.87-1.91	7	0.555	2083	0.527	1	97.7
1.91-1.94	8.6	0.489	2091	0.552	1	99.6
1.94-1.98	9.5	0.422	2088	0.571	1	99.5
1.98-2.03	9.9	0.346	2148	0.585	1	100
2.03-2.07	10.2	0.312	2093	0.612	1	100
2.07-2.12	10.2	0.256	2082	0.629	1	100
2.12-2.18	10.3	0.213	2138	0.645	1	100
2.18-2.25	10.3	0.176	2124	0.661	1	100
2.25-2.32	10.5	0.163	2118	0.654	1	100
2.32-2.4	10.5	0.14	2127	0.668	1	100
2.4-2.5	10.7	0.116	2131	0.687	1	100
2.5-2.61	10.8	0.108	2152	0.716	1	100
2.61-2.75	10.9	0.093	2145	0.862	1	100
2.75-2.92	10.9	0.078	2133	0.951	1	100
2.92-3.15	10.9	0.061	2151	0.934	1	100
3.15-3.46	10.9	0.045	2170	0.941	1	100
3.46-3.96	10.7	0.034	2166	0.914	1	100
3.96-4.99	10.5	0.029	2214	0.862	1	100
4.99-50	10	0.029	2336	0.903	1	99.7

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2E98

2e98

Resolution: 1.84→35.71 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.469 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2111	2129	5 %	RANDOM
R_work	0.1683	-	-	-
all	0.1704	44483	-	-
obs	0.1704	42354	98.96 %	-

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 max: 58.03 Å² / B_iso mean: 30.229 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.84→35.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3397	0	69	315	3781

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.021	3532
X-RAY DIFFRACTION	r_angle_refined_deg	1.901	1.939	4755
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.649	5	424
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.569	23.424	184
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.541	15	585
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.616	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.16	0.2	502
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2715
X-RAY DIFFRACTION	r_mcbond_it	1.231	1.5	2109
X-RAY DIFFRACTION	r_mcangle_it	2.049	2	3350
X-RAY DIFFRACTION	r_scbond_it	3.318	3	1423
X-RAY DIFFRACTION	r_scangle_it	5.185	4.5	1405

LS refinement shell

Resolution: 1.84→1.887 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	125	-
R_work	0.266	2706	-
all	-	2831	-
obs	-	-	91.56 %

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	2.6969	-2.3902	-0.0426	2.3736	0.5669	1.7746	0.1023	0.0606	-0.0312	-0.1484	-0.0485	-0.0281	0.1166	0.1636	-0.0538	0.1443	0.021	0.0218	0.1566	-0.0011	0.1686	21.129	2.581	18.068
2	5.9461	-8.9647	-2.8033	15.1908	3.8145	1.4255	-0.3001	-0.6852	-0.1365	0.2922	0.1818	0.0853	0.1814	0.5326	0.1183	0.123	0.1333	0.0134	0.5175	0.0733	0.1835	31.654	-2.662	23.326
3	2.2835	-0.4492	-0.5104	1.7694	0.45	2.3169	0.0867	-0.1015	0.1335	-0.0452	-0.0329	-0.1502	-0.1056	0.1862	-0.0538	0.1422	-0.0175	0.019	0.1499	0.0075	0.1476	20.661	12.894	22.403
4	5.9487	-3.9152	1.2097	2.594	-0.7923	0.2477	-0.0762	-0.3632	-0.8073	0.0357	0.3206	0.4684	0.0086	-0.0483	-0.2444	0.6193	0.1866	-0.3039	1.0621	-0.3542	0.6965	22.342	1.466	33.077
5	2.2058	-1.4867	-1.3576	5.2422	-0.2568	5.1193	-0.115	-0.3716	0.0717	0.043	0.0235	-0.4394	-0.1743	0.4861	0.0916	0.1181	-0.0344	-0.0211	0.2078	-0.0066	0.1553	22.878	16.983	34.009
6	2.1596	-0.4973	3.2388	0.9364	0.2973	6.2476	0.0891	-0.3367	-0.1496	0.1075	0.0817	0.0178	0.2262	-0.4505	-0.1707	0.1738	-0.0614	-0.0241	0.2146	0.0589	0.1407	13.683	2.011	39.909
7	0.9773	0.5557	0.6203	0.5931	0.6275	1.1014	0.0538	-0.163	-0.0293	0.0909	-0.0217	-0.0571	0.0231	-0.1055	-0.0321	0.1534	0.0009	0.0013	0.1678	0.0013	0.1236	12.724	8.794	33.513
8	1.7619	-0.0054	-2.2207	2.4359	-0.385	3.7411	0.1985	-0.1681	0.2276	0.4215	-0.0889	0.1293	-0.3015	-0.1632	-0.1096	0.1551	-0.0279	0.0754	0.2361	-0.0715	0.1242	-9.55	6.036	33.397
9	1.0478	0.355	0.1647	0.5641	0.2313	0.7809	-0.0027	-0.0027	0.0113	-0.0026	-0.0334	0.0131	-0.0116	-0.0291	0.0361	0.1417	0.0058	0.0146	0.1433	-0.0015	0.1372	10.6	5.397	18.224
10	10.4244	-6.3958	2.7281	5.8532	-1.9617	3.0465	0.3785	0.3417	0.0373	-0.9952	-0.1388	-0.2471	-0.3282	0.1909	-0.2396	0.4642	-0.0345	0.1222	0.1163	0.0096	0.1376	19.603	12.852	10.207
11	0.9065	0.2227	-0.4547	0.1408	0.1762	1.2436	-0.0426	-0.0383	-0.0819	0.0415	-0.0067	-0.0027	0.1281	0.0691	0.0493	0.1755	-0.0002	0.0182	0.1407	0.0093	0.1588	0.407	-7.687	4.151
12	2.0096	1.1793	-1.3411	9.3749	-4.1937	3.4671	0.0149	0.1984	0.1971	-0.0678	0.0973	0.3092	-0.1295	-0.078	-0.1123	0.1535	-0.0001	-0.0364	0.1574	0.0438	0.1327	-5.14	8.277	-10.512
13	0.9147	0.7441	0.0612	1.1117	-0.027	2.1618	-0.0387	0.0242	-0.0051	-0.0394	0.0498	0.0607	0.1207	-0.0897	-0.0111	0.1532	-0.0044	0.0056	0.1328	0.0036	0.1415	-4.69	-6.554	0.382
14	6.5164	2.4315	1.594	18.6785	5.9562	2.9144	-0.1476	0.3413	0.197	-0.9199	0.1099	0.1383	-0.4744	-0.1933	0.0377	0.2161	0.0857	0.0342	0.2024	0.0623	0.1732	-17.27	5.623	0.617
15	1.5651	0.5607	1.2659	4.5247	1.3007	1.2285	0.0126	-0.2455	-0.0295	-0.0454	0.0005	0.2886	0.0634	-0.2323	-0.0132	0.1519	-0.0747	-0.0024	0.1956	0.0324	0.1929	-16.402	-8.614	3.087
16	4.5267	-3.2409	-3.2253	22.632	3.7807	3.8226	-0.028	0.2253	0.0934	0.3955	0.0554	0.9831	-0.0474	-0.5804	-0.0274	0.0166	0.0212	0.0467	0.3957	0.0021	0.2741	-24.686	-0.783	8.38
17	0.2612	0.2204	0.1559	0.3175	0.4293	1.2044	-0.0214	-0.1269	0.0269	-0.0071	-0.0566	0.0907	0.0545	-0.1839	0.078	0.1316	-0.0127	0.0106	0.2071	0.0172	0.174	-11.671	-4.492	12.303
18	1.9579	0.3791	-1.9508	3.0352	-1.3086	2.8859	-0.0351	-0.073	-0.1052	0.2192	-0.0023	0.2872	-0.0063	-0.1291	0.0374	0.1563	-0.0547	0.0421	0.2203	0.0103	0.1156	-10.804	-4.953	32.278
19	0.3831	0.182	0.1861	0.1804	0.0834	1.4551	0.0261	-0.0507	-0.0001	0.0059	-0.0334	0.0172	0.0033	0.0252	0.0073	0.1425	0.0038	0.0142	0.1405	0.0085	0.1411	1.001	-1.853	9.583
20	3.4544	-1.871	2.8685	2.8468	-2.7201	4.568	0.078	0.1777	-0.1862	-0.0583	0.0063	-0.1112	0.1763	0.2474	-0.0842	0.1646	0.0366	0.0176	0.1212	-0.0179	0.151	7.19	-9.092	-0.648

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 34
2	X-RAY DIFFRACTION	2	A	35 - 49
3	X-RAY DIFFRACTION	3	A	50 - 69
4	X-RAY DIFFRACTION	4	A	70 - 95
5	X-RAY DIFFRACTION	5	A	96 - 107
6	X-RAY DIFFRACTION	6	A	108 - 122
7	X-RAY DIFFRACTION	7	A	123 - 151
8	X-RAY DIFFRACTION	8	A	152 - 178
9	X-RAY DIFFRACTION	9	A	179 - 223
10	X-RAY DIFFRACTION	10	A	224 - 239
11	X-RAY DIFFRACTION	11	B	13 - 29
12	X-RAY DIFFRACTION	12	B	30 - 48
13	X-RAY DIFFRACTION	13	B	49 - 72
14	X-RAY DIFFRACTION	14	B	80 - 94
15	X-RAY DIFFRACTION	15	B	95 - 114
16	X-RAY DIFFRACTION	16	B	115 - 128
17	X-RAY DIFFRACTION	17	B	129 - 155
18	X-RAY DIFFRACTION	18	B	156 - 179
19	X-RAY DIFFRACTION	19	B	180 - 222
20	X-RAY DIFFRACTION	20	B	223 - 240

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi