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- PDB-2eqa: Crystal Structure of the hypothetical Sua5 protein from Sulfolobu... -

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Basic information

Entry
Database: PDB / ID: 2eqa
TitleCrystal Structure of the hypothetical Sua5 protein from Sulfolobus tokodaii
ComponentsHypothetical protein ST1526Hypothesis
KeywordsRNA BINDING PROTEIN / YrdC/RibB fold / YrdC domain / Sua5 domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA processing / double-stranded RNA 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 / 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 / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsAgari, Y. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
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 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Hypothetical protein ST1526
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4543
Polymers39,0831
Non-polymers3722
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 Hypothetical protein ST1526 / Hypothesis / hypothetical Sua5 protein


Mass: 39082.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: strain7 / Gene: 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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium Acetate, 4.0M Sodium Nitrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97915, 0.9, 0.97973
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 7, 2006
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.91
30.979731
ReflectionResolution: 1.8→50 Å / Num. all: 32701 / Num. obs: 32701 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 52.47
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 12.1 / Num. unique all: 3212 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→36.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3041542.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3249 10 %RANDOM
Rwork0.208 ---
all0.211 ---
obs0.208 32611 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.22 Å2 / ksol: 0.39543 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 24 180 2768
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 538 10.1 %
Rwork0.216 4777 -
obs-5315 98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4amp_prodrug.paramamp_prodrug.top

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