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- PDB-3omw: Crystal structure of Ssu72, an essential eukaryotic phosphatase s... -

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Basic information

Entry
Database: PDB / ID: 3omw
TitleCrystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II
ComponentsCG14216
KeywordsHYDROLASE / phosphatase / low molecular weight protein tyrosine phosphatase / C-terminal domain of RNA polymerase II / dephosphorylate C-terminal domain of RNA polymerase II / RNA polymerase II / transcription factor IIB / Pta1 / CPF complex
Function / homology
Function and homology information


RNA polymerase II transcribes snRNA genes / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / myosin phosphatase activity / : / protein-serine/threonine phosphatase / phosphatase activity / nucleus
Similarity search - Function
Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Helix Hairpins / Response regulator / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA polymerase II subunit A C-terminal domain phosphatase SSU72
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8701 Å
AuthorsZhang, Y. / Zhang, M. / Zhang, Y.
CitationJournal: Biochem.J. / Year: 2011
Title: Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue.
Authors: Zhang, Y. / Zhang, M. / Zhang, Y.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: CG14216
B: CG14216
C: CG14216
D: CG14216


Theoretical massNumber of molelcules
Total (without water)88,9304
Polymers88,9304
Non-polymers00
Water27015
1
A: CG14216


Theoretical massNumber of molelcules
Total (without water)22,2321
Polymers22,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CG14216


Theoretical massNumber of molelcules
Total (without water)22,2321
Polymers22,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CG14216


Theoretical massNumber of molelcules
Total (without water)22,2321
Polymers22,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CG14216


Theoretical massNumber of molelcules
Total (without water)22,2321
Polymers22,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.100, 101.929, 65.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CG14216 / LD40846p


Mass: 22232.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG14216, Dmel_CG14216 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VWE4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 10% isopropanol, 14-18% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.85→48.7 Å / Num. all: 26297 / Num. obs: 24877 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.087 / Net I/σ(I): 21.8
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.767 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FMV

3fmv


Resolution: 2.8701→48.507 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 1194 5.09 %
Rwork0.2221 --
obs0.2253 23460 50.09 %
all-26297 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.682 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.4874 Å20 Å20 Å2
2---0.1059 Å2-0 Å2
3---10.5933 Å2
Refinement stepCycle: LAST / Resolution: 2.8701→48.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 0 15 6231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066316
X-RAY DIFFRACTIONf_angle_d0.9788492
X-RAY DIFFRACTIONf_dihedral_angle_d19.6972404
X-RAY DIFFRACTIONf_chiral_restr0.07932
X-RAY DIFFRACTIONf_plane_restr0.0031116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8701-2.9850.3741250.29352338X-RAY DIFFRACTION47
2.985-3.12080.39261280.29942489X-RAY DIFFRACTION50
3.1208-3.28530.32621260.27382502X-RAY DIFFRACTION50
3.2853-3.49110.35431420.24442455X-RAY DIFFRACTION50
3.4911-3.76060.24241170.21552507X-RAY DIFFRACTION50
3.7606-4.13880.27081610.20152428X-RAY DIFFRACTION50
4.1388-4.73730.23271230.17842488X-RAY DIFFRACTION50
4.7373-5.96680.26981490.19012478X-RAY DIFFRACTION50
5.9668-48.51340.26871230.20842581X-RAY DIFFRACTION52

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