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- PDB-4jbr: tRNA-guanine transglycosylase Y330C mutant as covalently linked d... -

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Basic information

Entry
Database: PDB / ID: 4jbr
TitletRNA-guanine transglycosylase Y330C mutant as covalently linked dimer in space group P6(5)22
ComponentstRNA-guanine transglycosylase
KeywordsTRANSFERASE / covalent dimer / TIM-barrel / guanine / preQ1 / tRNA
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine 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: 2.92 Å
AuthorsJakobi, S. / Klebe, G.
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface.
Authors: Nguyen, D. / Xie, X. / Jakobi, S. / Terwesten, F. / Metz, A. / Nguyen, T.X.P. / Palchykov, V.A. / Heine, A. / Reuter, K. / Klebe, G.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1533
Polymers43,0101
Non-polymers1442
Water2,180121
1
A: tRNA-guanine transglycosylase
hetero molecules

A: tRNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3076
Polymers86,0202
Non-polymers2874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1650 Å2
ΔGint-5 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.552, 127.552, 116.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

DetailsDimerization and formation of disulfidbridge upon crystallization, monomeric state in solution proven by native nanoESI-MS

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Components

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


Mass: 43009.797 Da / Num. of mol.: 1 / Mutation: Y330C
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: pASK-IBA13plus / 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID AT POSITION 312 IS LYS. SEE REUTER ET AL. [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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: MgAc 0.2M, PEG3350 20%; 2% DMSO and 10% glycerol in cryoprotection buffer, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2013 / Details: mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.92→30 Å / Num. all: 12637 / Num. obs: 12637 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 44.91 Å2 / Rsym value: 0.1
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 6.06 / Num. unique all: 619 / Rsym value: 0.441 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 2.92→28.111 Å / SU ML: 0.39 / Cross valid method: Rfree / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML / Details: TLS refinement in 7 groups
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 635 5.05 %random
Rwork0.2031 ---
obs0.2053 12578 99.81 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.56 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 46.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.9404 Å2-0 Å20 Å2
2---1.9404 Å20 Å2
3---3.8809 Å2
Refinement stepCycle: LAST / Resolution: 2.92→28.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 5 121 2908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032850
X-RAY DIFFRACTIONf_angle_d0.6653856
X-RAY DIFFRACTIONf_dihedral_angle_d12.2681009
X-RAY DIFFRACTIONf_chiral_restr0.041418
X-RAY DIFFRACTIONf_plane_restr0.003513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9202-3.14540.34591290.24332313X-RAY DIFFRACTION100
3.1454-3.46140.26771150.20652362X-RAY DIFFRACTION100
3.4614-3.9610.21791200.17712365X-RAY DIFFRACTION100
3.961-4.9860.191360.17582376X-RAY DIFFRACTION100
4.986-28.11180.27691350.23282527X-RAY DIFFRACTION99
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)
10.03930.05640.01520.07310.02740.0485-0.06580.0267-0.047-0.0041-0.1069-0.1071-0.0588-0.0822-0.00050.32320.0534-0.00750.2649-0.01210.27519.597840.2921-11.7112
20.02030.0049-0.02040.01940.01170.02930.07310.12670.06420.07510.0135-0.10290.0786-0.0011-00.3296-0.0571-0.0460.3118-0.05340.36926.227640.6282-6.6375
30.12350.003-0.15450.0035-0.01410.26190.07820.0666-0.04220.1126-0.0279-0.0188-0.01320.0010.17160.3361-0.1225-0.12660.1976-0.04330.255124.512947.31076.2469
40.0863-0.0011-0.00250.2067-0.08460.071-0.0112-0.06310.076-0.1144-0.1458-0.0184-0.0002-0.0901-0.49850.3496-0.05420.01710.1209-0.16580.126310.531952.9114.8845
50.02950.03340.01860.03210.02180.02410.0421-0.0885-0.0101-0.0774-0.1328-0.1141-0.0472-0.106700.32460.03740.00260.3689-0.09630.33470.216642.5371.0199
60.0272-0.0156-0.02110.00990.01270.01410.004-0.1063-0.12830.036-0.06110.1641-0.1134-0.0526-00.3297-0.0862-0.06310.36580.12540.48175.255817.1715-2.5439
70.0346-0.0096-0.02970.04170.00470.01580.1805-0.063-0.02630.0496-0.18010.01440.05720.024300.2658-0.0245-0.0220.28930.01560.31593.236523.7349-7.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 11:70)
2X-RAY DIFFRACTION2chain 'A' and (resseq 71:98)
3X-RAY DIFFRACTION3chain 'A' and (resseq 99:147)
4X-RAY DIFFRACTION4chain 'A' and (resseq 148:236)
5X-RAY DIFFRACTION5chain 'A' and (resseq 237:282)
6X-RAY DIFFRACTION6chain 'A' and (resseq 283:318)
7X-RAY DIFFRACTION7chain 'A' and (resseq 319:385)

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