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

ID or keywords:

Entry

Database: PDB / ID: 3sgv

Title

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1290

Components

Undecaprenyl pyrophosphate synthase

Keywords

TRANSFERASE / Alpha/beta

Function / homology

Function and homology information

Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 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	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	3sgv.cif.gz	199.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3sgv.ent.gz	161.3 KB	Display	PDB format
PDBx/mmJSON format	3sgv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3sgv_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	3sgv_full_validation.pdf.gz	1.6 MB	Display
Data in XML	3sgv_validation.xml.gz	25.6 KB	Display
Data in CIF	3sgv_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sg/3sgv ftp://data.pdbj.org/pub/pdb/validation_reports/sg/3sgv	HTTPS FTP

-
Related structure data

Related structure data	3sgtC 3sgxC 3sh0C 4h2jC 4h2mC 4h2oC 4h38C 4h3aC 4h3cC 4h8eC C: citing same article (ref.)
Similar structure data	5cqb-d 3qas-d 2e9c-d 3sh0-d 3tzy-2 1f75-d 6loi-1 5fzk-d 5kh2-2 3th8-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

59 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)	63.139, 69.004, 112.561
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

unknown

#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: b0174, ispU, JW0169, rth, uppS, yaeS / Production host: Escherichia coli (E. coli) References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical	ChemComp-2BJ / 2-{[3-(3,4-dimethylphenoxy)phenyl]carbamoyl}-4-nitrobenzoic acid Mass: 406.388 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₂H₁₈N₂O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.15 Å³/Da / Density % sol: 42.85 %
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-F / Wavelength: 0.9787 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 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: 1.61→50 Å / Num. obs: 62778 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.2 % / R_merge(I) obs: 0.095 / Χ²: 1.201 / Net I/σ(I): 7.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.61-1.64	5.6	0.704	2554	0.67	1	80.5
1.64-1.67	8.1	0.613	2805	0.415	1	88.2
1.67-1.7	10.7	0.577	2925	0.379	1	92.5
1.7-1.73	12.4	0.542	3058	0.395	1	96.3
1.73-1.77	13.7	0.463	3105	0.395	1	98.2
1.77-1.81	14.8	0.407	3148	0.421	1	98.7
1.81-1.86	15.6	0.381	3163	0.461	1	99.3
1.86-1.91	16.1	0.303	3185	0.513	1	99.7
1.91-1.97	16.4	0.247	3172	0.525	1	99.6
1.97-2.03	16.5	0.204	3193	0.53	1	99.7
2.03-2.1	16.6	0.176	3162	0.619	1	99.7
2.1-2.19	16.8	0.145	3189	0.747	1	99.7
2.19-2.28	17	0.131	3213	0.918	1	99.8
2.28-2.4	17.1	0.116	3190	1.001	1	99.8
2.4-2.56	17.4	0.105	3226	1.252	1	100
2.56-2.75	17.8	0.099	3238	1.56	1	100
2.75-3.03	18.1	0.094	3236	2.179	1	100
3.03-3.47	17.8	0.084	3275	2.909	1	100
3.47-4.37	17.3	0.065	3293	2.965	1	100
4.37-50	15.4	0.057	3448	2.879	1	99.1

-
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 / Resolution: 1.61→43.61 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.147 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / 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	0.2136	3146	5 %	RANDOM
R_work	0.1737	-	-	-
obs	0.1757	62528	97.27 %	-
all	-	65674	-	-

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: 63.19 Å² / B_iso mean: 25.583 Å² / B_iso min: 2.4 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.61→43.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3487	0	135	350	3972

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.021	3744
X-RAY DIFFRACTION	r_angle_refined_deg	2.249	1.964	5075
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.989	5	450
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.601	23.542	192
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.725	15	613
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.602	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.176	0.2	524
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	2967
X-RAY DIFFRACTION	r_mcbond_it	1.429	1.5	2187
X-RAY DIFFRACTION	r_mcangle_it	2.37	2	3485
X-RAY DIFFRACTION	r_scbond_it	3.807	3	1557
X-RAY DIFFRACTION	r_scangle_it	5.939	4.5	1583

LS refinement shell

Resolution: 1.611→1.653 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	195	-
R_work	0.283	3618	-
all	-	3813	-
obs	-	-	81.84 %

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	3.334	-1.2483	0.019	2.1493	0.0685	2.3685	-0.0161	0.1262	-0.1514	-0.1338	0.0089	-0.1209	0.0837	0.1874	0.0072	0.0502	-0.0121	0.0188	0.0899	-0.039	0.082	21.114	2.697	18.035
2	3.8816	-4.3677	-0.3872	10.2461	-0.7284	1.6392	-0.0262	0.0017	0.0501	0.0122	0.0013	-0.5655	0.0124	0.3823	0.0249	0.0307	-0.0091	-0.0013	0.1361	-0.0237	0.109	28.452	5.658	22.424
3	0.9514	-0.1314	0.5429	2.8835	0.2148	2.8146	0.0961	-0.1023	-0.1984	0.2442	0.0137	-0.2517	0.5584	0.1936	-0.1097	0.1566	0.0175	-0.0149	0.1069	0.003	0.1293	20.579	-1.555	31.087
4	2.9077	-1.2212	0.708	7.2837	-1.561	1.7135	-0.032	-0.1579	0.18	0.1142	-0.045	-0.6149	-0.0195	0.248	0.077	0.0608	-0.0251	-0.0061	0.1034	-0.04	0.1226	22.611	16.23	34.246
5	3.5558	0.4153	4.0294	0.0956	-0.1253	6.8099	0.3325	-0.4355	-0.3134	0.0122	0.0266	-0.0323	0.4742	-0.5592	-0.3591	0.125	-0.0526	-0.0021	0.1749	0.0209	0.1038	14.262	2.075	39.16
6	1.6714	-2.1209	0.6644	7.9594	-3.673	3.288	-0.1349	-0.3513	-0.0544	0.6034	0.1936	-0.0277	-0.171	-0.1815	-0.0586	0.1476	0.0043	-0.0154	0.1623	-0.0181	0.0821	17.136	11.095	41.784
7	1.208	1.2226	0.4745	1.7182	0.4803	0.8176	0.0821	-0.0836	0.0498	0.1434	-0.0991	0.0436	0.0444	-0.2075	0.017	0.0515	-0.0202	0.0162	0.0944	-0.0239	0.0456	8.232	6.375	29.939
8	4.7189	0.6067	-2.4765	4.7681	-1.1652	4.5428	0.2693	-0.3984	0.505	0.5566	-0.0184	0.396	-0.4719	-0.1211	-0.2509	0.1448	-0.0169	0.1316	0.1453	-0.1091	0.182	-10.202	7.183	33.564
9	1.2312	0.5787	0.3467	1.3315	0.3314	1.1437	-0.0281	-0.0392	0.0619	0.0316	-0.0106	0.1187	-0.0247	-0.0496	0.0387	0.0519	-0.006	0.0134	0.0697	-0.0218	0.0637	8.034	6.155	18.898
10	2.4292	-0.7107	0.6562	3.9782	1.1047	1.7815	-0.0173	0.3242	0.1457	-0.4828	0.0106	-0.1665	-0.3416	0.1954	0.0068	0.1081	-0.0375	0.0421	0.1155	-0.0011	0.0519	21.186	9.028	11.705
11	1.7838	0.4186	-0.4028	1.7909	0.0837	2.1599	-0.0861	0.0029	-0.2368	0.0797	0.0039	-0.0062	0.2475	0.1512	0.0822	0.0859	-0.0029	0.0123	0.0796	-0.0044	0.079	0.971	-9.607	5.421
12	5.0717	1.6391	-0.5438	9.5966	-4.0857	4.0236	-0.0088	0.3592	0.3746	-0.0608	0.0589	0.2153	-0.1759	-0.064	-0.0501	0.091	0.0022	-0.0298	0.1169	0.0453	0.0634	-5.235	8.922	-9.801
13	1.6384	0.1553	-0.286	2.4455	-0.5944	3.2453	-0.0335	0.094	0.1124	-0.1064	0.051	0.1351	0.0464	-0.1533	-0.0175	0.0428	-0.035	-0.0127	0.0699	-0.0021	0.081	-7.373	-5.452	-0.737
14	4.1605	0.4406	-0.4314	3.9654	-1.2041	2.291	0.0135	0.2531	0.4286	-0.303	0.1402	0.481	-0.0679	-0.3817	-0.1537	0.0995	-0.0458	-0.0315	0.1369	0.0289	0.1707	-17.945	-8.601	-1.171
15	11.9782	-0.538	1.8258	6.3968	1.0394	5.2551	-0.0495	-0.3742	0.8732	0.1242	-0.1713	0.9155	-0.3322	-1.0303	0.2208	0.0651	0.0569	0.0487	0.2972	-0.0686	0.3157	-21.922	0.854	9.616
16	3.3101	1.1665	-0.6748	3.9045	0.5408	3.3344	0.0116	-0.086	0.062	0.2016	-0.0491	0.3475	0.1378	-0.5545	0.0375	0.0625	-0.0605	0.0083	0.1477	0.0061	0.091	-16.927	-10.632	6.272
17	0.79	-0.4832	-0.5102	2.1935	-1.1845	2.4915	0.0166	-0.0775	-0.0069	0.211	0.0524	0.4424	0.0278	-0.2386	-0.069	0.0864	-0.0408	0.0869	0.1534	-0.0566	0.1783	-12.495	0.126	25.78
18	6.6754	0.5167	-4.24	3.6707	-1.3644	2.7312	-0.1031	-0.593	-0.1657	0.1483	0.0618	0.1623	0.056	0.3655	0.0413	0.1568	-0.0208	0.0452	0.2224	0.0263	0.0925	-5.972	-6.99	31.573
19	0.7558	0.1996	0.1948	0.5041	0.2163	1.6901	-0.0048	-0.024	0.0479	0.0066	-0.0166	0.0723	-0.0152	0.1026	0.0215	0.0421	-0.0079	0.0084	0.0481	-0.0061	0.0469	1.36	-1.781	8.452
20	3.927	-0.7633	3.5622	3.0379	-0.5039	6.3662	0.0732	0.1976	-0.1654	0.0787	0.0393	-0.1947	0.3052	0.4821	-0.1125	0.0766	0.0328	0.0174	0.0935	-0.0187	0.068	7.888	-10.342	0.276

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 - 61
3	X-RAY DIFFRACTION	3	A	62 - 92
4	X-RAY DIFFRACTION	4	A	93 - 107
5	X-RAY DIFFRACTION	5	A	108 - 120
6	X-RAY DIFFRACTION	6	A	121 - 132
7	X-RAY DIFFRACTION	7	A	133 - 155
8	X-RAY DIFFRACTION	8	A	156 - 179
9	X-RAY DIFFRACTION	9	A	180 - 215
10	X-RAY DIFFRACTION	10	A	216 - 238
11	X-RAY DIFFRACTION	11	B	13 - 27
12	X-RAY DIFFRACTION	12	B	28 - 46
13	X-RAY DIFFRACTION	13	B	47 - 88
14	X-RAY DIFFRACTION	14	B	89 - 107
15	X-RAY DIFFRACTION	15	B	108 - 123
16	X-RAY DIFFRACTION	16	B	124 - 142
17	X-RAY DIFFRACTION	17	B	143 - 167
18	X-RAY DIFFRACTION	18	B	168 - 180
19	X-RAY DIFFRACTION	19	B	181 - 224
20	X-RAY DIFFRACTION	20	B	225 - 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://pdbjlvh1.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