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- PDB-1vdx: Crystal Structure of a Pyrococcus horikoshii protein with similar... -

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Basic information

Entry
Database: PDB / ID: 1vdx
TitleCrystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase
ComponentsHypothetical protein PH0099
KeywordsLIGASE / Structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


RNA 2',3'-cyclic 3'-phosphodiesterase / RNA 2',3'-cyclic 3'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
Similarity search - Function
Phosphoesterase, HXTX / LigT like Phosphoesterase / RNA 2',3'-cyclic phosphodiesterase / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRehse, P.H. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.
Authors: Rehse, P.H. / Tahirov, T.H.
History
DepositionMar 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PH0099
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1662
Polymers21,1311
Non-polymers351
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.068, 45.471, 93.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein PH0099 / 2'-5' RNA ligase related protein


Mass: 21130.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O57823, RNA ligase (ATP)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: MES, PEG 4000, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 2, 2003
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 7670 / Num. obs: 7670 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.36 / Num. unique all: 7670 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IUH.pdb

1iuh


Resolution: 2.4→39.84 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 399182.78 / 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
Rfree0.274 552 7.5 %RANDOM
Rwork0.225 ---
obs0.225 7386 95.3 %-
all-7386 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.3079 Å2 / ksol: 0.344613 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.96 Å20 Å20 Å2
2---2.81 Å20 Å2
3----3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 1 41 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it3.291.5
X-RAY DIFFRACTIONc_mcangle_it4.82
X-RAY DIFFRACTIONc_scbond_it5.242
X-RAY DIFFRACTIONc_scangle_it7.132.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 83 7.4 %
Rwork0.277 1045 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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