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- PDB-4rdi: Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine d... -

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Basic information

Entry
Database: PDB / ID: 4rdi
TitleCrystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA
ComponentstRNA threonylcarbamoyladenosine dehydratase
KeywordsLIGASE / Rossmann Fold / Dehydratase
Function / homology
Function and homology information


Ligases; Forming carbon-oxygen bonds / tRNA threonylcarbamoyladenosine dehydratase / cyclic threonylcarbamoyladenosine biosynthetic process / ubiquitin-like modifier activating enzyme activity / sodium ion binding / potassium ion binding / protein homodimerization activity / ATP binding / membrane
Similarity search - Function
ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / tRNA threonylcarbamoyladenosine dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPark, S.Y. / Kim, S. / Lee, H.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity.
Authors: Kim, S. / Lee, H. / Park, S.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 16, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: tRNA threonylcarbamoyladenosine dehydratase
B: tRNA threonylcarbamoyladenosine dehydratase
C: tRNA threonylcarbamoyladenosine dehydratase
D: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,34212
Polymers124,9454
Non-polymers2,3978
Water10,989610
1
A: tRNA threonylcarbamoyladenosine dehydratase
B: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6716
Polymers62,4732
Non-polymers1,1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-26 kcal/mol
Surface area18550 Å2
MethodPISA
2
C: tRNA threonylcarbamoyladenosine dehydratase
D: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6716
Polymers62,4732
Non-polymers1,1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-23 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.710, 97.036, 84.215
Angle α, β, γ (deg.)90.00, 111.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tRNA threonylcarbamoyladenosine dehydratase / t(6)A37 dehydratase


Mass: 31236.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tcdA, ygdL, csdL / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46927, Ligases; Forming carbon-oxygen bonds
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG 3350, 0.1 M Tris, pH 8.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 70428 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.81 / Rsym value: 0.362 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.442 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20916 3545 5 %RANDOM
Rwork0.15631 ---
obs0.15897 66826 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å2-0.55 Å2
2--0.08 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 148 610 8044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197575
X-RAY DIFFRACTIONr_bond_other_d0.0010.027418
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.98610281
X-RAY DIFFRACTIONr_angle_other_deg0.895316961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61723.401297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.201151186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2011560
X-RAY DIFFRACTIONr_chiral_restr0.1160.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021695
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_it2.4052.3313890
X-RAY DIFFRACTIONr_mcbond_other2.4052.333889
X-RAY DIFFRACTIONr_mcangle_it3.4093.4734850
X-RAY DIFFRACTIONr_mcangle_other3.4093.4754851
X-RAY DIFFRACTIONr_scbond_it3.3932.7583685
X-RAY DIFFRACTIONr_scbond_other3.3922.7583685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0173.9565429
X-RAY DIFFRACTIONr_long_range_B_refined7.44620.1379118
X-RAY DIFFRACTIONr_long_range_B_other7.06519.6598800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 271 -
Rwork0.195 4811 -
obs--96.98 %

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