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- PDB-4l56: tRNA guanine transglycosylase H333D mutant apo structure -

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Basic information

Entry
Database: PDB / ID: 4l56
TitletRNA guanine transglycosylase H333D mutant apo structure
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / DIMER INTERFACE / GLYCOSYLTRANSFERASE / TRNA PROCESSING / METAL-BINDING / QUEUOSINE / tRNA / ZINC BINDING / GUANINE BINDING
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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNguyen, T.X.P. / Heine, A. / Klebe, G.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt.
Authors: Jakobi, S. / Nguyen, P.T. / Debaene, F. / Cianferani, S. / Reuter, K. / Klebe, G.
History
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7419
Polymers43,0311
Non-polymers7108
Water4,918273
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,48218
Polymers86,0622
Non-polymers1,42016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area1940 Å2
ΔGint-6 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.049, 65.198, 69.547
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 43030.773 Da / Num. of mol.: 1 / Mutation: H333D
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: pRP-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODONPLUS-RIPL
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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris 10% DMSO 7% PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.85507 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2012 / Details: Silicon, active surface 50 nm Rh-coated
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85507 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 46368 / Num. obs: 46368 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.068 / Net I/σ(I): 18
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2246 / Rsym value: 0.495 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PUD

1pud


Resolution: 1.7→29.391 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.31 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 2335 5.04 %random
Rwork0.1601 ---
obs0.1614 46321 99.01 %-
all-46368 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→29.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 43 273 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132935
X-RAY DIFFRACTIONf_angle_d1.4063959
X-RAY DIFFRACTIONf_dihedral_angle_d12.9011077
X-RAY DIFFRACTIONf_chiral_restr0.1417
X-RAY DIFFRACTIONf_plane_restr0.008524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73180.2746930.22262449X-RAY DIFFRACTION94
1.7318-1.76940.26491400.20712572X-RAY DIFFRACTION100
1.7694-1.81060.23171400.18912621X-RAY DIFFRACTION100
1.8106-1.85590.22141270.1782589X-RAY DIFFRACTION100
1.8559-1.9060.19561530.16642590X-RAY DIFFRACTION100
1.906-1.96210.1921450.15762595X-RAY DIFFRACTION100
1.9621-2.02540.20111410.15212601X-RAY DIFFRACTION100
2.0254-2.09780.16681470.14812587X-RAY DIFFRACTION100
2.0978-2.18180.15741250.14262633X-RAY DIFFRACTION100
2.1818-2.2810.20421310.14882596X-RAY DIFFRACTION100
2.281-2.40120.1781440.1472630X-RAY DIFFRACTION100
2.4012-2.55160.2091190.15692599X-RAY DIFFRACTION100
2.5516-2.74850.15411540.15752607X-RAY DIFFRACTION100
2.7485-3.02480.23081300.16682596X-RAY DIFFRACTION99
3.0248-3.46190.17171570.15542566X-RAY DIFFRACTION99
3.4619-4.35940.15881480.14472608X-RAY DIFFRACTION99
4.3594-29.3950.17381410.17542547X-RAY DIFFRACTION95
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)
11.04830.07910.24220.8730.53241.735-0.03890.22780.0951-0.2246-0.12180.2102-0.2575-0.3132-0.14110.03610.0046-0.04050.05870.00310.07581.863311.68889.8845
20.6249-0.3801-0.0811.05630.63310.93680.0594-0.00820.0806-0.05870.0252-0.1167-0.17360.06420.13820.0587-0.01250.00630.04010.00160.073716.664814.877894.8683
30.0598-0.1552-0.2021.1729-0.35920.76170.0370.15590.1096-0.64610.0586-0.15390.168-0.03420.36710.1937-0.01580.00620.11640.0438-0.001612.0698.480966.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:160)
2X-RAY DIFFRACTION2(chain A and resid 161:281)
3X-RAY DIFFRACTION3(chain A and resid 282:383)

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