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- PDB-4ydu: Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4ydu
TitleCrystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP
Components
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsTRANSFERASE / YgjD-YeaZ complex / t6A transferase
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'-DIPHOSPHATE / : / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsZhang, W. / Collinet, B. / Perrochia, L. / Durand, D. / Van Tilbeurgh, H.
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
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionMar 4, 2015ID: 4WOS
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)128,46225
Polymers125,8264
Non-polymers2,63721
Water7,891438
1
A: tRNA N6-adenosine threonylcarbamoyltransferase
C: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20212
Polymers62,9132
Non-polymers1,28910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA N6-adenosine threonylcarbamoyltransferase
D: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,26113
Polymers62,9132
Non-polymers1,34811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.620, 68.480, 87.070
Angle α, β, γ (deg.)109.38, 92.66, 117.66
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 4

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 3362 - 336
21ALAALABB2 - 3362 - 336
12GLYGLYCC2 - 2292 - 229
22GLYGLYDD2 - 2292 - 229

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999348, -0.010999, -0.03438), (-0.012022, -0.999487, -0.0297), (-0.034035, 0.030094, -0.998967)31.03395, 85.02357, -73.11006

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 36879.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tsaD, gcp, ygjD, b3064, JW3036 / Production host: Escherichia coli (E. coli) / References: UniProt: P05852, EC: 2.6.99.4
#2: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / YeaZ / 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) / Gene: tsaB, yeaZ, b1807, JW1796
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P76256

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Non-polymers , 5 types, 459 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.46 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% PEG4000, 0.3M Lithium Sulfate, 0.1 M Sodium Acetate and 0.1 M HEPES
PH range: 7.2 - 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.25→49.38 Å / Num. obs: 55653 / % possible obs: 97.9 % / Redundancy: 3.97 % / Rsym value: 0.121 / Net I/σ(I): 11
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.46 / Rsym value: 0.483 / % possible all: 95.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IVP

2ivp


Resolution: 2.33→49.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.862 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25265 2783 5 %RANDOM
Rwork0.20229 ---
obs0.20479 52870 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.15 Å2-0.05 Å2
2--0.08 Å20.53 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.33→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8410 0 164 438 9012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198753
X-RAY DIFFRACTIONr_bond_other_d0.0080.028288
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.98211914
X-RAY DIFFRACTIONr_angle_other_deg0.777318992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01651129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59623.642335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.955151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8381556
X-RAY DIFFRACTIONr_chiral_restr0.0850.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219933
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021909
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_it1.9182.4144541
X-RAY DIFFRACTIONr_mcbond_other1.9012.4064527
X-RAY DIFFRACTIONr_mcangle_it2.7843.6025653
X-RAY DIFFRACTIONr_mcangle_other2.7843.6025654
X-RAY DIFFRACTIONr_scbond_it2.7272.7384212
X-RAY DIFFRACTIONr_scbond_other2.7272.7384213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0313.9896262
X-RAY DIFFRACTIONr_long_range_B_refined5.2155.10510337
X-RAY DIFFRACTIONr_long_range_B_other5.1675.08410217
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
11B4834medium positional0.280.5
22B3334medium positional0.410.5
11D4834medium thermal2.682
22D3334medium thermal2.872
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 201 -
Rwork0.236 3818 -
obs--95.06 %
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)
10.6676-0.10630.23130.82790.24472.0776-0.0472-0.26110.02220.1160.09170.0648-0.0354-0.2581-0.04450.03910.0225-0.00440.15190.04130.06156.44634.856-22.067
20.780.11790.34710.36820.19861.5686-0.02310.0929-0.0623-0.02880.02870.0274-0.01740.0237-0.00560.02620.0090.01790.04110.02990.0537-25.82652.035-48.606
31.3572-0.53860.09151.7098-0.23751.26230.06520.10220.0564-0.0786-0.03770.0148-0.0369-0.1145-0.02750.02610.00490.00030.05990.02850.01542.48240.952-60.642
41.10960.401-0.26341.3152-0.73082.0080.0092-0.04340.02150.01960.0109-0.0058-0.0218-0.0241-0.02010.0270.02820.0160.03560.01890.013-28.69144.647-10.42
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 336
2X-RAY DIFFRACTION2B1 - 338
3X-RAY DIFFRACTION3C1 - 230
4X-RAY DIFFRACTION4D1 - 229

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