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- PDB-5ce7: Structure of a non-canonical CID of Ctk3 -

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Basic information

Entry
Database: PDB / ID: 5ce7
TitleStructure of a non-canonical CID of Ctk3
ComponentsCTD kinase subunit gamma
KeywordsTRANSCRIPTION / Lsg1 / CTD kinase subunit gamma / right-handed superhelix
Function / homology
Function and homology information


CTDK-1 complex / positive regulation of DNA-templated transcription, elongation / positive regulation of transcription by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase II / mRNA processing / calcium ion binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
CTD kinase subunit gamma Ctk3, N-terminal / CTD kinase subunit gamma CTK3 / CTD kinase subunit gamma Ctk3, C-terminal / CTD kinase subunit gamma / CTD kinase subunit gamma CTK3 C-terminus / CID domain / CID domain profile. / ENTH/VHS
Similarity search - Domain/homology
CTD kinase subunit gamma
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMuehlbacher, W. / Mayer, A. / Sun, M. / Remmert, M. / Cheung, A.C. / Niesser, J. / Soeding, J. / Cramer, P.
CitationJournal: Proteins / Year: 2015
Title: Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold.
Authors: Muhlbacher, W. / Mayer, A. / Sun, M. / Remmert, M. / Cheung, A.C. / Niesser, J. / Soeding, J. / Cramer, P.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: CTD kinase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4623
Polymers15,9851
Non-polymers4772
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint9 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.310, 51.310, 119.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CTD kinase subunit gamma / CTDK-I gamma subunit / CTD kinase subunit 3


Mass: 15985.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: ctk3, SPCC4B3.08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USJ8
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4 / Details: PEG 6000, citric acid, lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97964, 0.98012 ,0.97197
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979641
20.980121
30.971971
ReflectionNumber: 157934 / Rmerge(I) obs: 0.077 / Χ2: 0.99 / D res high: 2 Å / Num. obs: 20524 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.9547.1223310.022
6.338.9542210.027
5.166.3352810.033
4.475.1665110.03
44.4773710.028
3.65480410.034
3.383.6587410.041
3.163.3894410.054
2.983.16101410.071
2.832.98105210.081
2.72.83110110.105
2.582.7115510.114
2.482.58124810.136
2.392.48126910.169
2.312.39131210.186
2.242.31132510.23
2.172.24141710.274
2.112.17144910.334
2.052.11143310.377
22.05155610.456
ReflectionResolution: 2→47.12 Å / Num. obs: 20524 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge F obs: 0.082 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Χ2: 0.991 / Net I/σ(I): 20.89 / Num. measured all: 157934
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.3280.4564.9312233155715560.48899.9
2.05-2.110.2760.3775.8911238143314330.403100
2.11-2.170.2470.3346.6111177145014490.35899.9
2.17-2.240.2120.2747.710459141714170.295100
2.24-2.310.1580.239.239949132613250.24799.9
2.31-2.390.1240.18611.6510440131213120.199100
2.39-2.480.1170.16912.2310067126912690.181100
2.48-2.580.0890.13614.799666124812480.146100
2.58-2.70.080.11416.638618115511550.123100
2.7-2.830.0710.10518.178182110211010.11399.9
2.83-2.980.0530.08122.948420105210520.087100
2.98-3.160.0460.07125.998052101410140.076100
3.16-3.380.0360.05432.0173289449440.057100
3.38-3.650.0270.04138.2763478748740.044100
3.65-40.020.03448.3163028048040.037100
4-4.470.0160.02854.1657377377370.03100
4.47-5.160.0160.0352.2647396516510.032100
5.16-6.330.020.03348.7740005285280.036100
6.33-8.950.0170.02752.8232454224220.029100
8.950.0110.02270.4317352332330.023100

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.73 / FOM acentric: 0.73 / FOM centric: 0.72 / Reflection: 5863 / Reflection acentric: 4453 / Reflection centric: 1410
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-47.120.90.950.87279119160
4.5-7.10.880.90.85799533266
3.6-4.50.870.890.81976725251
3.1-3.60.80.820.76995780215
2.7-3.10.640.650.5817391407332
2.5-2.70.510.520.471075889186

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→47.12 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 983 4.79 %Random selection
Rwork0.1894 ---
obs0.1917 20524 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 30 67 1194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081145
X-RAY DIFFRACTIONf_angle_d1.0471544
X-RAY DIFFRACTIONf_dihedral_angle_d17.952439
X-RAY DIFFRACTIONf_chiral_restr0.072168
X-RAY DIFFRACTIONf_plane_restr0.005197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.10560.26271540.19162757X-RAY DIFFRACTION100
2.1056-2.23760.24891300.18512842X-RAY DIFFRACTION100
2.2376-2.41030.24051450.17372754X-RAY DIFFRACTION100
2.4103-2.65280.21021640.17122777X-RAY DIFFRACTION100
2.6528-3.03670.24381400.17742812X-RAY DIFFRACTION100
3.0367-3.82560.26421290.20122790X-RAY DIFFRACTION100
3.8256-47.13290.22861210.20012809X-RAY DIFFRACTION100

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