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- PDB-4wq5: YgjD(V85E)-YeaZ heterodimer in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 4wq5
TitleYgjD(V85E)-YeaZ heterodimer in complex with ATP
Components
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsTRANSFERASE / heterodimer / YgjD-YeaZ / Val85Glu / t6A
Function / homology
Function and homology information


glycosylation-dependent protein binding / N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / maintenance of translational fidelity / metallopeptidase activity / iron ion binding / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / : / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å
AuthorsZhang, W.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.
Authors: Zhang, W. / Collinet, B. / Perrochia, L. / Durand, D. / van Tilbeurgh, H.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA N6-adenosine threonylcarbamoyltransferase
B: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,62519
Polymers125,8864
Non-polymers1,73915
Water2,072115
1
A: tRNA N6-adenosine threonylcarbamoyltransferase
D: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,88411
Polymers62,9432
Non-polymers9429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-55 kcal/mol
Surface area21540 Å2
MethodPISA
2
B: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7408
Polymers62,9432
Non-polymers7986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-55 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.690, 68.080, 87.340
Angle α, β, γ (deg.)109.31, 92.56, 117.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 331
2010B1 - 331
1020C1 - 229
2020D1 - 229

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein tRNA N6-adenosine threonylcarbamoyltransferase / N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine ...N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD / tRNA threonylcarbamoyladenosine biosynthesis protein TsaD


Mass: 36909.219 Da / Num. of mol.: 2 / Mutation: V85E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsaD, gcp, ygjD, b3064, JW3036
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P05852, EC: 2.6.99.4
#2: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaB


Mass: 26033.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsaB, yeaZ, b1807, JW1796
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P76256

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Non-polymers , 6 types, 130 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 26% PEG4000, 0.3 M Lithium Sulfate and 0.1 Sodium Acetate

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 48866 / % possible obs: 96 % / Redundancy: 3.34 % / Net I/σ(I): 13.06

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementResolution: 2.33→42.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.35 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23323 2530 5 %RANDOM
Rwork0.17981 ---
obs0.1825 48069 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.13 Å2-0.13 Å2
2--0.74 Å20.76 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.33→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8153 0 104 115 8372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198428
X-RAY DIFFRACTIONr_bond_other_d0.0080.027875
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.97111483
X-RAY DIFFRACTIONr_angle_other_deg1.348318017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19951118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57923.579299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.233151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0651547
X-RAY DIFFRACTIONr_chiral_restr0.0730.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0219650
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021831
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8165.3884495
X-RAY DIFFRACTIONr_mcbond_other3.8045.3844488
X-RAY DIFFRACTIONr_mcangle_it4.9089.0885602
X-RAY DIFFRACTIONr_mcangle_other4.9089.095603
X-RAY DIFFRACTIONr_scbond_it5.0475.7753933
X-RAY DIFFRACTIONr_scbond_other5.0475.7753934
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5859.545882
X-RAY DIFFRACTIONr_long_range_B_refined7.75213.16936020
X-RAY DIFFRACTIONr_long_range_B_other7.75213.16936021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A167100.14
12B167100.14
21C122750.15
22D122750.15
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 145 -
Rwork0.267 2755 -
obs--74.17 %

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