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- PDB-1hru: THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 1hru
TitleTHE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI
ComponentsYRDC GENE PRODUCT
KeywordsUNKNOWN FUNCTION / protein folding / structural genomics / RNA / Sua5 / YrdC / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / regulation of translational fidelity / nucleotidyltransferase activity / rRNA processing / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Threonylcarbamoyl-AMP synthase / : / 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 / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsTeplova, M. / Tereshko, V. / Sanishvili, R. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2000
Title: The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding.
Authors: Teplova, M. / Tereshko, V. / Sanishvili, R. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M.
History
DepositionDec 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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_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_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: YRDC GENE PRODUCT
B: YRDC GENE PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5804
Polymers41,3912
Non-polymers1902
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.500, 71.650, 55.280
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein YRDC GENE PRODUCT / 20.8 KDA PROTEIN IN AROE-SMG INTERGENIC REGION


Mass: 20695.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YRDC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: P45748
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: sodium potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.6 Msodium potassium phosphate1reservoir
31

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9794, 0.9465
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 26, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
30.94651
ReflectionResolution: 1.96→30 Å / Num. all: 62780 / Num. obs: 62780 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.6
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.6 / Num. unique all: 23642 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 230966
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→22.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 345209.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5212 10.2 %RANDOM
Rwork0.202 ---
obs0.202 51213 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.84 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å27.08 Å2
2---5.13 Å20 Å2
3---4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→22.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 10 386 3241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.012
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 780 10.3 %
Rwork0.217 6806 -
obs--74.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3PARION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.217

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