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- PDB-4e1b: Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus to... -

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Basic information

Entry
Database: PDB / ID: 4e1b
TitleRe-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus tokodaii with bound threonylcarbamoyladenylate
ComponentsYrdC/Sua5 family protein
KeywordsRNA BINDING PROTEIN / YRDC/RIBB fold / YRDC domain / SUA5 domain / tRNA modification T6A
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA processing / regulation of translational fidelity / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Threonylcarbamoyl-AMP synthase, C-terminal domain / tRNA threonylcarbamoyladenosine biosynthesis protein SUA5 / Threonylcarbamoyl-AMP synthase, C-terminal domain / Threonylcarbamoyl-AMP synthase, C-terminal domain superfamily / Threonylcarbamoyl-AMP synthase, C-terminal domain / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase ...Threonylcarbamoyl-AMP synthase, C-terminal domain / tRNA threonylcarbamoyladenosine biosynthesis protein SUA5 / Threonylcarbamoyl-AMP synthase, C-terminal domain / Threonylcarbamoyl-AMP synthase, C-terminal domain superfamily / Threonylcarbamoyl-AMP synthase, C-terminal domain / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / DHBP synthase / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
threonylcarbamoyladenylate / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsParthier, C. / Goerlich, S. / Jaenecke, F. / Breithaupt, C. / Braeuer, U. / Fandrich, U. / Clausnitzer, D. / Wehmeier, U.F. / Boettcher, C. / Scheel, D. / Stubbs, M.T.
CitationJournal: Proteins / Year: 2008
Title: X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7.
Authors: Agari, Y. / Sato, S. / Wakamatsu, T. / Bessho, Y. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Shinkai, A.
History
DepositionMar 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4E1B REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R2EQASF ...THIS ENTRY 4E1B REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R2EQASF DETERMINED BY THE AUTHORS OF THE PDB ENTRY 2EQA: Y.AGARI,A.SHINKAI,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YrdC/Sua5 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5993
Polymers39,0831
Non-polymers5172
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.391, 120.843, 67.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein YrdC/Sua5 family protein / protein ST1546


Mass: 39082.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: STK_15260, SUA5 / Plasmid: pET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL-X / References: UniProt: Q970S6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TXA / threonylcarbamoyladenylate


Mass: 492.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N6O11P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.23 Å3/Da / Density % sol: 44.83 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2EQA.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→34.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.24 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21698 3249 10 %RANDOM
Rwork0.18297 ---
all0.18634 29361 --
obs0.18634 29361 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 34 178 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2772.0013601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08224.579107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9521515
X-RAY DIFFRACTIONr_chiral_restr0.1580.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211935
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3021.51647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21122683
X-RAY DIFFRACTIONr_scbond_it3.56331000
X-RAY DIFFRACTIONr_scangle_it5.6684.5915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 249 -
Rwork0.204 2146 -
obs--99.75 %

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