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- PDB-4pum: tRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4pum
TitletRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
Keywordstransferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / preQ1 / tRNA / transferase-transferase inhibitor complex
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
Queuine tRNA-ribosyltransferase-like / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2WU / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme.
Authors: Neeb, M. / Czodrowski, P. / Heine, A. / Barandun, L.J. / Hohn, C. / Diederich, F. / Klebe, G.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5495
Polymers43,0691
Non-polymers4804
Water3,945219
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,09710
Polymers86,1382
Non-polymers9608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area5470 Å2
ΔGint-11 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.690, 64.660, 70.770
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

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Components

#1: Protein Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 43068.844 Da / Num. of mol.: 1 / Mutation: D156N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2-ZM-D156N / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2WU / 6-amino-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 230.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. ...AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995))

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.93→80 Å / Num. all: 30236 / Num. obs: 30236 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.047 / Net I/σ(I): 21.6
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.505 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.93→70.668 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 1511 5 %
Rwork0.1592 --
obs0.1614 30214 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→70.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 30 219 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072951
X-RAY DIFFRACTIONf_angle_d1.0443988
X-RAY DIFFRACTIONf_dihedral_angle_d13.4121096
X-RAY DIFFRACTIONf_chiral_restr0.069421
X-RAY DIFFRACTIONf_plane_restr0.005550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.99230.26961390.23412637X-RAY DIFFRACTION99
1.9923-2.06350.29621350.20912563X-RAY DIFFRACTION99
2.0635-2.14620.21051380.18642620X-RAY DIFFRACTION99
2.1462-2.24390.23931360.18322586X-RAY DIFFRACTION99
2.2439-2.36220.22731360.16842582X-RAY DIFFRACTION98
2.3622-2.51020.2321380.16272613X-RAY DIFFRACTION99
2.5102-2.7040.20681360.1562583X-RAY DIFFRACTION99
2.704-2.97610.19311370.15262615X-RAY DIFFRACTION99
2.9761-3.40670.18951380.14692620X-RAY DIFFRACTION99
3.4067-4.29210.18491380.13732632X-RAY DIFFRACTION99
4.2921-70.7150.17451400.15662652X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.242-0.2957-0.00940.45150.04241.3272-0.0161-0.11410.14650.15180.0158-0.0216-0.1642-0.00830.00260.1608-0.00210.0170.1281-0.0140.147598.18127.66319.2384
22.09120.016-0.39411.64940.60442.40260.0098-0.22180.22420.22990.0364-0.1507-0.29210.0472-0.04960.2480.0162-0.03860.2193-0.03420.1614108.095214.324927.7036
30.8979-0.29511.22170.4826-0.64861.8194-0.01660.13890.0364-0.0292-0.0313-0.1338-0.0750.25780.0440.127-0.01320.030.1881-0.00960.1713107.44057.9118-0.7922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 383 )

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