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- PDB-4e85: crystal STRUCTURE OF HAT DOMAIN OF RNA14 -

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Basic information

Entry
Database: PDB / ID: 4.0E+85
Titlecrystal STRUCTURE OF HAT DOMAIN OF RNA14
ComponentsmRNA 3'-end-processing protein RNA14
KeywordsSTRUCTURAL PROTEIN / HAT domain / HEAT repeat / Rna15
Function / homology
Function and homology information


mRNA 3'-end processing / mRNA binding / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / mRNA 3'-end-processing protein Rna14-like / Suppressor of forked / Suppressor of forked protein (Suf) / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
mRNA 3'-end-processing protein RNA14
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPaulson, A.R. / Tong, L.
CitationJournal: Rna / Year: 2012
Title: Crystal structure of the Rna14-Rna15 complex.
Authors: Paulson, A.R. / Tong, L.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA 3'-end-processing protein RNA14
B: mRNA 3'-end-processing protein RNA14


Theoretical massNumber of molelcules
Total (without water)159,2552
Polymers159,2552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-32 kcal/mol
Surface area52540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.870, 241.730, 49.020
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 mRNA 3'-end-processing protein RNA14


Mass: 79627.414 Da / Num. of mol.: 2 / Fragment: UNP residues 18-661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: RNA14, KLLA0F26290g / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CII8

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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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES 7.5, 13% PEG 3350, 1% tryptone, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 29000 / Num. obs: 26572 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.6742
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.44 / % possible all: 67.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
COMOphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E6H

4e6h


Resolution: 3→46.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 565484.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1195 4.8 %RANDOM
Rwork0.233 ---
obs0.233 24884 87.8 %-
all-28000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.1879 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 72.9 Å2
Baniso -1Baniso -2Baniso -3
1--20.61 Å20 Å20 Å2
2--8.8 Å20 Å2
3---11.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 3→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9221 0 0 0 9221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.49 81 4.8 %
Rwork0.412 1611 -
obs--60.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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