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- PDB-2ond: Crystal Structure of the HAT-C domain of murine CstF-77 -

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Basic information

Entry
Database: PDB / ID: 2ond
TitleCrystal Structure of the HAT-C domain of murine CstF-77
ComponentsCleavage stimulation factor 77 kDa subunit
KeywordsSTRUCTURAL PROTEIN / HAT domain
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / Processing of Capped Intron-Containing Pre-mRNA / mRNA cleavage stimulating factor complex / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA 3'-end processing / mRNA binding / nucleoplasm / nucleus
Similarity search - Function
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 / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Cleavage stimulation factor subunit 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsBai, Y. / Auperin, T.C. / Chou, C.-Y. / Chang, G.-G. / Manley, J.L. / Tong, L.
CitationJournal: Mol.Cell / Year: 2007
Title: Crystal Structure of Murine CstF-77: Dimeric Association and Implications for Polyadenylation of mRNA Precursors.
Authors: Bai, Y. / Auperin, T.C. / Chou, C.Y. / Chang, G.G. / Manley, J.L. / Tong, L.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cleavage stimulation factor 77 kDa subunit
B: Cleavage stimulation factor 77 kDa subunit


Theoretical massNumber of molelcules
Total (without water)73,2652
Polymers73,2652
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-25 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.400, 155.400, 161.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Cleavage stimulation factor 77 kDa subunit / CSTF 77 kDa subunit / CF-1 77 kDa subunit / CstF-77


Mass: 36632.531 Da / Num. of mol.: 2 / Fragment: residues 242-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cstf3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q99LI7

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: with protease (subtilisin) in the drop, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 53540 / % possible obs: 99.5 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 35.5688
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 6.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 360403.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3852 7.4 %RANDOM
Rwork0.224 ---
obs0.224 52247 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.3067 Å2 / ksol: 0.350414 e/Å3
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å28.86 Å20 Å2
2--0.65 Å20 Å2
3----1.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5099 0 0 0 5099
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.492.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.413 338 6.8 %
Rwork0.348 4608 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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