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- PDB-4wq4: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 4wq4
TitleE. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP
Components
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsTRANSFERASE / heterodimer / YgjD-YeaZ / Glu12Ala / t6A
Function / homology
Function and homology information


glycosylation-dependent protein binding / N6-L-threonylcarbamoyladenine synthase / tRNA 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 / : / DI(HYDROXYETHYL)ETHER / 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. / Collinet, B.
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)127,25813
Polymers125,7104
Non-polymers1,5489
Water5,080282
1
A: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6757
Polymers62,8552
Non-polymers8205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-40 kcal/mol
Surface area21960 Å2
MethodPISA
2
B: tRNA N6-adenosine threonylcarbamoyltransferase
D: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5836
Polymers62,8552
Non-polymers7284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-36 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.270, 68.070, 87.130
Angle α, β, γ (deg.)109.30, 92.98, 117.23
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
1114A1 - 338
2114B1 - 338
1124C2 - 229
2124D2 - 229

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999633, -0.014421, -0.022929), (-0.013919, -0.999663, 0.021892), (-0.023237, -0.021565, -0.999497)31.85079, -88.54234, 66.90257

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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: 36821.203 Da / Num. of mol.: 2 / Mutation: E12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsaD, gcp, ygjD, b3064, JW3036 / Plasmid: pET21a-YGJD-E12A
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 (E. coli) / References: UniProt: P76256

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Non-polymers , 6 types, 291 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: 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
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH7.5, 25% PEG4000, 0.3 M Lithium Sulfate, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 49021 / % possible obs: 96.9 % / Redundancy: 3.18 % / Net I/σ(I): 11.42

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementResolution: 2.33→49.04 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.247 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25265 2451 5 %RANDOM
Rwork0.20229 ---
obs0.20479 46561 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.47 Å20.52 Å2
2--0.81 Å20.3 Å2
3----1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.33→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8337 0 92 282 8711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198604
X-RAY DIFFRACTIONr_bond_other_d0.010.028136
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.97311717
X-RAY DIFFRACTIONr_angle_other_deg0.851318659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73251127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85524.074324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.281151313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9071547
X-RAY DIFFRACTIONr_chiral_restr0.080.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0219798
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021857
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_it3.1164.2284522
X-RAY DIFFRACTIONr_mcbond_other3.1134.2284519
X-RAY DIFFRACTIONr_mcangle_it4.2717.1295643
X-RAY DIFFRACTIONr_mcangle_other4.2717.135644
X-RAY DIFFRACTIONr_scbond_it3.9374.6054082
X-RAY DIFFRACTIONr_scbond_other3.9384.6054082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.297.5886075
X-RAY DIFFRACTIONr_long_range_B_refined6.2649.6449948
X-RAY DIFFRACTIONr_long_range_B_other6.2649.6449949
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B4776medium positional0.330.5
22D3279medium positional0.420.5
11B4776medium thermal4.445
22D3279medium thermal4.255
LS refinement shellResolution: 2.331→2.392 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 163 -
Rwork0.336 3098 -
obs--87.73 %

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