PDB-3qas: Structure of Undecaprenyl Diphosphate synthase

ID or keywords:

Entry

Database: PDB / ID: 3qas

Title

Structure of Undecaprenyl Diphosphate synthase

Components

Undecaprenyl pyrophosphate synthase

Keywords

TRANSFERASE / alpha-helix / Isoprenoid Biosynthesis

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: 1.7 Å

Authors

Cao, R. / Oldfield, E.

Citation

Journal: Chem.Biol.Drug Des. / Year: 2011
Title: Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target.
Authors: Sinko, W. / de Oliveira, C. / Williams, S. / Van Wynsberghe, A. / Durrant, J.D. / Cao, R. / Oldfield, E. / McCammon, J.A.

History

Deposition	Jan 11, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qas.cif.gz	190.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3qas.ent.gz	152.7 KB	Display	PDB format
PDBx/mmJSON format	3qas.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qas_validation.pdf.gz	437.8 KB	Display	wwPDB validaton report
Full document	3qas_full_validation.pdf.gz	447 KB	Display
Data in XML	3qas_validation.xml.gz	21.8 KB	Display
Data in CIF	3qas_validation.cif.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qa/3qas ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qas	HTTPS FTP

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Related structure data

Related structure data	2e99S S: Starting model for refinement
Similar structure data	5cqb-d 3sh0-d 3sgx-d 5cqj-d 5kh2-2 2e9c-d 4h38-d 3th8-d 3sgt-d 3sgv-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

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	62.633, 68.762, 111.816
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
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 / Production host: Escherichia coli (E. coli) References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H₂O

#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 / Production host:

Escherichia coli (E. coli)
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 344 / 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: 41.8 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

Diffraction	Mean temperature: 123 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 50646 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / R_merge(I) obs: 0.051 / Net I/σ(I): 51.2
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Starting model: 2.0E+99 / Resolution: 1.7→27.95 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.942 / SU B: 4.325 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	2711	5.1 %	RANDOM
R_work	0.184	-	-	-
obs	0.186	50646	99.5 %	-
all	-	53420	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 28.989 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0 Å²	0 Å²
2-	-	-0.13 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→27.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3451	0	0	344	3795

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.021	3522
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.115	1.92	4757
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.912	5	431
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.08	23.492	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.18	15	595
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.322	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.18	0.2	508
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	2732
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	1.517	1.5	2141
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.592	2	3403
X-RAY DIFFRACTION	r_scbond_it	3.869	3	1381
X-RAY DIFFRACTION	r_scangle_it	6.198	4.5	1354
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.75 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	197	-
R_work	0.292	3532	-
obs	-	-	95.59 %

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	0.9291	-1.0103	0.339	1.0415	0.0417	0.9356	0.0986	0.0712	0.0011	-0.065	-0.0931	-0.0149	0.0716	0.0807	-0.0055	0.1428	0.0161	0.0092	0.147	-0.0025	0.1711	20.967	2.5295	18.1606
2	1.6122	-2.4004	-1.2958	5.6024	0.3183	0.7646	-0.071	-0.2733	0.0408	0.0681	0.1048	-0.123	-0.0291	0.4084	-0.0337	0.0999	0.0347	-0.0146	0.238	-0.0042	0.1635	29.5143	2.2639	23.2413
3	1.0577	-0.1105	0.198	0.3257	0.2676	1.0133	0.1046	-0.0635	-0.1019	0.0331	-0.0721	-0.0593	0.1329	-0.0031	-0.0325	0.1578	-0.0077	0.0055	0.1417	0.0147	0.1669	17.2885	3.0123	22.5481
4	0.182	-0.3105	0.4432	2.1623	0.0202	1.8007	-0.0211	-0.1411	0.0341	0.0306	0.1637	-0.0547	0.203	0.1325	-0.1426	0.1486	0.0195	-0.0127	0.1758	-0.0083	0.135	21.2564	5.5311	34.2844
5	1.7706	-1.0188	2.5501	1.3964	-1.1108	3.8889	0.0855	-0.3053	-0.0696	-0.0091	0.1221	0.0543	0.2115	-0.4074	-0.2076	0.1617	-0.0368	0.0045	0.1957	0.035	0.1219	13.837	1.5861	39.2418
6	2.29	-0.8948	1.8434	2.2187	-0.5332	1.5744	0.0403	-0.3358	0.0638	0.4064	-0.0186	-0.0374	-0.0032	-0.2859	-0.0218	0.1989	-0.0149	0.0024	0.2364	-0.0294	0.1056	17.1087	9.3187	42.5921
7	0.5649	0.6764	0.5599	0.946	0.7248	0.8356	0.0597	-0.0728	0.0102	0.1005	-0.0064	-0.0342	0.0273	-0.1135	-0.0532	0.1533	-0.0043	0.0022	0.1537	-0.006	0.1422	12.1224	9.0526	30.7653
8	1.9594	-0.7988	-1.5225	1.6419	-0.1964	4.6448	0.2173	-0.142	0.1679	0.4448	-0.1454	0.0594	-0.4142	-0.1131	-0.072	0.2308	-0.0753	0.0989	0.2228	-0.0707	0.1223	-9.7045	5.3922	33.7663
9	0.8029	0.321	0.2296	0.2764	0.1967	0.3634	0.0205	-0.0198	0.0355	0.009	-0.0433	0.0273	0.0015	-0.0346	0.0228	0.1395	0.0068	0.0133	0.1468	-0.0064	0.1503	9.2349	5.6952	18.7859
10	6.3818	-3.978	1.2706	2.6924	-0.6663	1.4826	0.3124	0.2355	-0.0525	-0.5694	-0.1238	-0.1004	-0.2711	0.1601	-0.1886	0.2991	-0.01	0.0646	0.122	0.0129	0.1371	20.1643	12.1251	10.3694
11	0.5634	0.0441	-0.4218	-0.1228	-0.2696	0.9424	-0.052	0.007	-0.0841	-0.0122	-0.0114	0.0746	0.0649	0.0335	0.0634	0.1641	-0.0036	-0.0011	0.1398	0.0138	0.1642	0.2613	-7.7897	4.1306
12	0.8007	-0.217	0.5344	9.618	-5.0014	2.8177	-0.0395	0.2966	0.1247	0.1888	0.1129	0.0616	-0.156	0.0083	-0.0734	0.1655	0.007	-0.0344	0.1295	0.0544	0.1319	-4.7619	9.785	-10.4481
13	0.688	0.3969	0.0074	1.5492	-0.9684	1.995	-0.0469	0.0684	-0.0209	-0.1508	0.0403	0.0455	0.2488	-0.1276	0.0066	0.1672	-0.0181	-0.0043	0.1301	0.0008	0.1549	-5.3367	-9.0571	-2.0399
14	5.8925	3.0361	3.2711	3.9695	4.2017	3.0321	-0.3469	-0.195	0.7041	-0.6004	-0.0657	0.4555	-0.4246	-0.1885	0.4126	0.261	-0.0486	-0.1274	0.1427	0.0919	0.2554	-14.7819	0.4531	0.4712
15	2.7126	2.7527	0.6189	5.045	0.9999	-0.0582	-0.0359	-0.0681	0.0709	-0.1189	0.1241	0.1026	0.1713	-0.2225	-0.0882	0.182	-0.1362	-0.0433	0.2255	0.0552	0.1508	-15.3504	-11.6417	2.454
16	20.6807	3.2852	6.9189	6.1709	-3.1056	-0.4553	-0.6534	-0.1665	1.2167	0.5784	0.7156	0.9193	-0.0236	0.0049	-0.0622	0.0752	0.1722	0.0071	0.4216	-0.1063	0.3433	-22.1235	4.5429	11.1243
17	1.031	0.08	0.2211	2.7727	0.9819	1.25	-0.0896	-0.1143	0.0434	0.0718	0.0762	0.2264	0.0842	-0.2636	0.0134	0.1146	-0.0407	0.0075	0.2001	0.0437	0.1719	-18.8211	-8.0242	6.3271
18	0.3909	-0.2998	-0.7767	1.2841	-1.0273	1.7523	0.0267	-0.0397	-0.009	0.051	-0.0372	0.1543	0.0342	-0.1648	0.0105	0.1277	-0.0698	0.0249	0.2586	-0.0298	0.1463	-10.2261	-2.3913	27.9613
19	0.4831	0.1889	0.2318	0.1603	-0.0314	0.9976	0.0274	-0.0358	0.0007	-0.0225	-0.0403	0.0193	0.005	0.0274	0.0129	0.1452	0.0023	0.0061	0.1408	0.0054	0.143	1.0193	-2.1546	7.9665
20	2.7397	-1.5305	3.4452	2.1299	-1.5887	3.9257	0.1118	0.1739	-0.0579	-0.0603	0.0034	-0.1331	0.267	0.1683	-0.1152	0.1809	0.0453	0.0074	0.134	-0.0075	0.1574	8.7666	-10.7418	1.5022

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 - 56
3	X-RAY DIFFRACTION	3	A	57 - 77
4	X-RAY DIFFRACTION	4	A	78 - 107
5	X-RAY DIFFRACTION	5	A	108 - 121
6	X-RAY DIFFRACTION	6	A	122 - 128
7	X-RAY DIFFRACTION	7	A	129 - 150
8	X-RAY DIFFRACTION	8	A	151 - 175
9	X-RAY DIFFRACTION	9	A	176 - 222
10	X-RAY DIFFRACTION	10	A	223 - 239
11	X-RAY DIFFRACTION	11	B	13 - 29
12	X-RAY DIFFRACTION	12	B	30 - 44
13	X-RAY DIFFRACTION	13	B	45 - 67
14	X-RAY DIFFRACTION	14	B	68 - 98
15	X-RAY DIFFRACTION	15	B	99 - 110
16	X-RAY DIFFRACTION	16	B	111 - 119
17	X-RAY DIFFRACTION	17	B	120 - 143
18	X-RAY DIFFRACTION	18	B	144 - 179
19	X-RAY DIFFRACTION	19	B	180 - 226
20	X-RAY DIFFRACTION	20	B	227 - 240

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