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- PDB-6n9a: Crystal Structure of Thermotoga maritima threonylcarbamoyladenosi... -

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Basic information

Entry
Database: PDB / ID: 6n9a
TitleCrystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP
Components
  • (tRNA threonylcarbamoyladenosine biosynthesis protein ...) x 2
  • tRNA N6-adenosine threonylcarbamoyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Threonylcarbamoyl transfer complex / t6A biosynthesis / tRNA modification
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #200 / tRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Nucleotidyltransferase; domain 5 - #200 / tRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2-(2-ETHOXYETHOXY)ETHANOL / ADENOSINE-5'-TRIPHOSPHATE / Chem-KG4 / TRIETHYLENE GLYCOL / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSwairjo, M.A. / Stec, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM110588-05 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Conformational communication mediates the reset step in t6A biosynthesis.
Authors: Luthra, A. / Paranagama, N. / Swinehart, W. / Bayooz, S. / Phan, P. / Quach, V. / Schiffer, J.M. / Stec, B. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionDec 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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 / 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
B: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D: tRNA N6-adenosine threonylcarbamoyltransferase
E: tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,85510
Polymers78,1553
Non-polymers1,7007
Water2,882160
1
B: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D: tRNA N6-adenosine threonylcarbamoyltransferase
E: tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
hetero molecules

B: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D: tRNA N6-adenosine threonylcarbamoyltransferase
E: tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,71020
Polymers156,3106
Non-polymers3,39914
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area16760 Å2
ΔGint-168 kcal/mol
Surface area56710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.053, 124.053, 119.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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TRNA threonylcarbamoyladenosine biosynthesis protein ... , 2 types, 2 molecules BE

#1: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaB


Mass: 23461.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tsaB, TM_0874, Tmari_0876 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZX7
#3: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaE


Mass: 18678.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1632 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1W7

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Protein , 1 types, 1 molecules D

#2: 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: 36015.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tsaD, gcp, TM_0145 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WXZ2, N6-L-threonylcarbamoyladenine synthase

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Non-polymers , 8 types, 167 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL / 2-(2-Ethoxyethoxy)ethanol


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#6: Chemical ChemComp-KG4 / 5'-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine


Mass: 391.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N5O9P
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 uL sample solution containing 3.1 mg/mL protein, 50 mM Tris (pH 7.5), 50 mM NaCl, 1 mM ATP and 0.1 mM MgCl2 with 2 uL reservoir solution containing 8% polyethylene glycol (PEG) 400, 100 mM ...Details: 2 uL sample solution containing 3.1 mg/mL protein, 50 mM Tris (pH 7.5), 50 mM NaCl, 1 mM ATP and 0.1 mM MgCl2 with 2 uL reservoir solution containing 8% polyethylene glycol (PEG) 400, 100 mM KCl, 50 mM MES (pH 6.0) and 0.8 mM MgCl2

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 2, 2016
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.5→107.43 Å / Num. obs: 36821 / % possible obs: 98.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Χ2: 1.082 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.542.61.88615410.1821.2812.2970.5584.2
2.54-2.593.92.12417830.2131.152.4320.50194.9
2.59-2.6461.96517880.2380.8412.1460.54299.1
2.64-2.698.81.55118400.5710.5421.6460.58199.5
2.69-2.759.71.33318220.6520.4441.4060.57499.9
2.75-2.8210.11.10118370.7580.361.1590.611100
2.82-2.8910.20.87818560.8050.2870.9240.655100
2.89-2.9610.30.75818590.8660.2460.7970.687100
2.96-3.0510.30.55718100.9230.180.5860.802100
3.05-3.1510.40.45218660.9380.1460.4760.892100
3.15-3.2610.40.35218390.9630.1140.371.052100
3.26-3.3910.40.30218430.9760.0980.3181.198100
3.39-3.5510.30.25118700.9830.0830.2651.381100
3.55-3.73100.18418760.9880.0610.1941.481100
3.73-3.979.70.15218470.9920.0520.1611.549100
3.97-4.279.10.11418770.9940.0410.1211.698100
4.27-4.718.60.08618660.9960.0320.0921.693100
4.71-5.398.80.08119170.9960.0290.0861.672100
5.39-6.799.30.07918840.9970.0280.0841.386100
6.79-107.438.90.0620000.9970.0210.0631.19499.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6A

2a6a


Resolution: 2.5→42.94 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.957 / SU B: 23.429 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21438 1787 5.4 %RANDOM
Rwork0.12185 ---
obs0.12681 31308 89.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.982 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0.83 Å2-0 Å2
2---1.66 Å20 Å2
3---5.38 Å2
Refinement stepCycle: 1 / Resolution: 2.5→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 105 161 5756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0145696
X-RAY DIFFRACTIONr_bond_other_d00.0175383
X-RAY DIFFRACTIONr_angle_refined_deg0.7831.6787706
X-RAY DIFFRACTIONr_angle_other_deg0.771.64912596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73922.731271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.962151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6911533
X-RAY DIFFRACTIONr_chiral_restr0.040.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.026225
X-RAY DIFFRACTIONr_gen_planes_other00.02983
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_it10.647.3712805
X-RAY DIFFRACTIONr_mcbond_other10.6437.3692804
X-RAY DIFFRACTIONr_mcangle_it13.93311.073501
X-RAY DIFFRACTIONr_mcangle_other13.93211.0733502
X-RAY DIFFRACTIONr_scbond_it13.3158.2892891
X-RAY DIFFRACTIONr_scbond_other13.3058.292891
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.52312.1024206
X-RAY DIFFRACTIONr_long_range_B_refined17.05187.2476119
X-RAY DIFFRACTIONr_long_range_B_other17.04787.2366111
X-RAY DIFFRACTIONr_rigid_bond_restr2.686311078
X-RAY DIFFRACTIONr_sphericity_free47.744591
X-RAY DIFFRACTIONr_sphericity_bonded43.476511048
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 83 -
Rwork0.368 1500 -
obs--58.01 %

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