PDB-5i07: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi...

ID or keywords:

Entry

Database: PDB / ID: 5i07

Title

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-Amino-4-(2-phenylethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Components

Queuine tRNA-ribosyltransferase

Keywords

TRANSFERASE / co-crystallization / shigellosis / TRANSFERASE INHIBITOR

Function / homology

Function and homology information

tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) biosynthetic process / metal ion binding / cytosol
Similarity search - Function

Biological species

Zymomonas mobilis subsp. mobilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Ehrmann, F.R. / Nguyen, D. / Heine, A. / Klebe, G.

Citation

Journal: To be Published
Title: Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors
Authors: Ehrmann, F.R. / Stojko, J. / Heine, A. / Diederich, F. / Reiter, K. / Sanglier-Cianferani, S. / Klebe, G.

History

Deposition	Feb 3, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jan 10, 2024	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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PDBx/mmCIF format	5i07.cif.gz	302.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5i07.ent.gz	245.4 KB	Display	PDB format
PDBx/mmJSON format	5i07.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5i07_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5i07_full_validation.pdf.gz	1 MB	Display
Data in XML	5i07_validation.xml.gz	31.7 KB	Display
Data in CIF	5i07_validation.cif.gz	46.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/5i07 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i07	HTTPS FTP

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Related structure data

Related structure data	5i00C 5i02C 5i03C 5i06C 5i09C 1p0dS 1y5v 1y5w 1y5x 3eos 3ge7 4fr6 4fsa 4kwo 4leq 4puk C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5lpq-d 5lpt-d 1lld-d 3vcm-d 2fgl-d 6ryl-d 6ncg-d 4q5j-d 3iau-d 2eg5-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Queuine tRNA-ribosyltransferase

B: Queuine tRNA-ribosyltransferase

hetero molecules

87.1 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)	69.133, 78.854, 85.171
Angle α, β, γ (deg.)	90.00, 108.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase Mass: 42925.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria) Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

#1: Protein

Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase

Mass: 42925.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Gene: tgt, ZMO0363 / Production host:

Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 5 types, 442 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-NE8 / 6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE Mass: 305.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₅N₅O
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.55 Å³/Da / Density % sol: 51.82 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.89→19.87 Å / Num. obs: 67732 / % possible obs: 98.3 % / Redundancy: 4.3 % / R_sym value: 0.082 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.89→2.01 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.493 / Mean I/σ(I) obs: 2.7 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1-2155_1492	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d

Resolution: 1.89→19.87 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.37

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	3386	5 %	random selection
R_work	0.1912	-	-	-
obs	0.1926	67714	98.49 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.89→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5618	0	80	432	6130

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5932
X-RAY DIFFRACTION	f_angle_d	0.858	7992
X-RAY DIFFRACTION	f_dihedral_angle_d	17.498	3576
X-RAY DIFFRACTION	f_chiral_restr	0.051	831
X-RAY DIFFRACTION	f_plane_restr	0.006	1116

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 (%)
1.8947-1.9217	0.3101	123	0.256	2333	X-RAY DIFFRACTION	86
1.9217-1.9504	0.2502	140	0.2364	2660	X-RAY DIFFRACTION	99
1.9504-1.9808	0.2555	144	0.2302	2731	X-RAY DIFFRACTION	99
1.9808-2.0133	0.2571	139	0.2292	2651	X-RAY DIFFRACTION	99
2.0133-2.0479	0.2722	140	0.2242	2650	X-RAY DIFFRACTION	99
2.0479-2.0852	0.2479	142	0.215	2698	X-RAY DIFFRACTION	99
2.0852-2.1252	0.2567	141	0.205	2672	X-RAY DIFFRACTION	99
2.1252-2.1685	0.2321	141	0.196	2684	X-RAY DIFFRACTION	99
2.1685-2.2156	0.2557	142	0.1916	2709	X-RAY DIFFRACTION	99
2.2156-2.2671	0.2324	142	0.2004	2682	X-RAY DIFFRACTION	99
2.2671-2.3237	0.2254	143	0.1979	2716	X-RAY DIFFRACTION	99
2.3237-2.3864	0.2377	141	0.1953	2696	X-RAY DIFFRACTION	99
2.3864-2.4565	0.2674	141	0.191	2663	X-RAY DIFFRACTION	99
2.4565-2.5357	0.2009	141	0.1946	2682	X-RAY DIFFRACTION	99
2.5357-2.6261	0.2481	142	0.1935	2694	X-RAY DIFFRACTION	99
2.6261-2.731	0.2002	141	0.1885	2682	X-RAY DIFFRACTION	99
2.731-2.855	0.2228	141	0.1924	2686	X-RAY DIFFRACTION	98
2.855-3.005	0.225	143	0.1933	2706	X-RAY DIFFRACTION	99
3.005-3.1925	0.2332	141	0.1989	2680	X-RAY DIFFRACTION	99
3.1925-3.4379	0.2004	143	0.1845	2732	X-RAY DIFFRACTION	99
3.4379-3.7817	0.2135	143	0.1772	2707	X-RAY DIFFRACTION	99
3.7817-4.324	0.1922	144	0.1696	2735	X-RAY DIFFRACTION	99
4.324-5.4293	0.1679	143	0.163	2722	X-RAY DIFFRACTION	99
5.4293-19.8715	0.2215	145	0.203	2757	X-RAY DIFFRACTION	98

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	0.4047	-0.4803	0.2026	1.3965	0.668	1.1009	0.0884	0.0214	-0.006	-0.1446	0.0175	-0.2807	-0.0696	0.0809	-0.091	0.1212	-0.0226	0.025	0.2045	-0.0021	0.2999	3.7939	-11.0504	78.2108
2	3.026	1.5422	3.4803	1.6879	1.6523	4.1507	0.4451	0.2578	-0.3891	0.0704	-0.0939	-0.1404	0.4305	0.3294	-0.377	0.1819	0.0026	-0.0527	0.2489	0.0267	0.3379	-7.4036	-33.2325	80.7537
3	1.5008	0.1559	-0.0759	1.1528	-0.0299	3.0666	0.1359	-0.1039	-0.0396	0.0194	0.1076	-0.3427	0.1206	0.3067	-0.2106	0.114	-0.001	-0.0285	0.1869	-0.0275	0.3192	3.3001	-24.3408	82.6728
4	0.3169	-0.0428	-0.0006	2.0939	0.0933	1.3313	0.0832	-0.2043	-0.052	0.2383	0.0078	-0.0845	0.0807	-0.0176	-0.0912	0.1242	-0.0334	-0.0454	0.2058	0.0066	0.2316	-3.3662	-16.2796	92.6214
5	1.8541	0.6079	2.6571	1.0207	0.6112	4.8531	-0.0393	0.055	0.086	-0.0732	0.0063	-0.0284	-0.145	-0.0499	0.034	0.1068	0.0163	0.0294	0.1724	-0.0141	0.216	-14.929	3.577	75.592
6	1.0401	0.6972	0.752	1.5556	0.249	0.8116	0.011	0.0034	-0.1384	-0.0622	0.0059	-0.219	-0.0229	0.0518	-0.0174	0.2155	0.0067	0.0489	0.1886	-0.0137	0.2121	-13.8493	-16.8561	44.0827
7	0.0675	0.0646	0.1111	0.4447	0.142	0.8547	0.0428	0.0261	0.0026	-0.1051	-0.0983	-0.0139	-0.2948	0.149	0.0406	0.3704	0.0373	-0.0317	0.2746	-0.0176	0.2187	-22.556	5.2415	51.7426
8	1.5048	0.0595	0.1582	1.6304	-0.0548	1.1834	-0.1036	0.1756	0.0092	-0.2077	0.0928	-0.0892	-0.3036	0.003	-0.0093	0.3061	-0.018	0.0288	0.2145	-0.0101	0.1924	-17.8033	-3.5346	41.9182
9	0.7754	0.1405	0.1377	1.9917	-0.029	0.7497	-0.0382	0.0861	-0.0021	-0.1788	0.0058	0.2142	-0.1473	-0.2164	0.0278	0.2321	0.0224	-0.0349	0.2077	-0.02	0.1573	-29.7795	-11.6478	41.5326
10	0.2505	-0.3536	0.1397	0.6412	-0.0957	1.9423	-0.005	-0.0226	-0.0667	-0.0624	0.0229	-0.0077	0.1173	-0.0105	-0.0143	0.1621	-0.0271	0.0168	0.203	0.0016	0.2121	-22.3461	-31.4917	60.9504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 11:105)
2	X-RAY DIFFRACTION	2	(chain A and resid 106:135)
3	X-RAY DIFFRACTION	3	(chain A and resid 136:159)
4	X-RAY DIFFRACTION	4	(chain A and resid 160:289)
5	X-RAY DIFFRACTION	5	(chain A and resid 290:382)
6	X-RAY DIFFRACTION	6	(chain B and resid 11:105)
7	X-RAY DIFFRACTION	7	(chain B and resid 106:135)
8	X-RAY DIFFRACTION	8	(chain B and resid 136:159)
9	X-RAY DIFFRACTION	9	(chain B and resid 160:289)
10	X-RAY DIFFRACTION	10	(chain B and resid 290:382)

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